Mercurial > repos > iracooke > tpp_prophets
changeset 18:84b47300a4c8 draft default tip
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:46:16 -0400 |
| parents | b68f292b2904 |
| children | |
| files | README README.md README.rst interprophet.xml peptide_prophet.xml pepxml_to_table.xml protein_prophet.xml protxml_to_table.xml repository_dependencies.xml test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml tool_dependencies.xml |
| diffstat | 12 files changed, 2203 insertions(+), 265 deletions(-) [+] |
line wrap: on
line diff
--- a/README Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -This package installs wrapper scripts for Peptide Prophet, iProphet and Protein Prophet - -Requirements: -This package uses protk and the tpp which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file
--- a/README.md Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition files and wrapper scripts for Peptide and Protein inference tools in the [Trans Proteomic Pipeline](http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP) (Peptide Prophet, iProphet and Protein Prophet). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -All the tools depend on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,37 @@ +TPP Prophets +============ + +Galaxy wrappers for Peptide Prophet, iProphet and Protein Prophet + +Requirements +------------ + +This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + +Please visit the TPP__ website for details of the various Prophet tools + +__ trans_proteomic_pipeline_
--- a/interprophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/interprophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,59 +1,71 @@ -<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.0.1"> - - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> - </requirements> - - - <description>Combine Peptide Prophet results from multiple search engines</description> - - <command>interprophet.rb --galaxy +<tool id="proteomics_search_interprophet_1" name="InterProphet" version="1.1.1"> + <description>Combine Peptide Prophet results from multiple search engines</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command> +<![CDATA[ + interprophet.rb --galaxy + #if str( $input_type.type ) == "files": + #for $pepxml_file in $input_type.pepxml_files: + ${pepxml_file} + #end for + #else + #for $list_item in $input_type.pepxml_list: + ${list_item} + #end for + #for $extra_list_holder in $input_type.extra_pepxml_lists: + #for $list_item in $extra_list_holder.extra_list: + ${list_item} + #end for + #end for + #end if - -o interprophet_output.pep.xml - - $use_nss - - $use_nrs - - $use_nse - - $use_nsi - - $use_nsm - - --p-thresh $p_thresh + -o interprophet_output.pep.xml + $use_nss + $use_nrs + $use_nse + $use_nsi + $use_nsm + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" - --threads $threads - -#for $pepxml_file in $pepxml_files: - ${pepxml_file} -#end for - - </command> - - - <inputs> - - <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> +]]> + </command> + <inputs> - <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/> - <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/> - <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/> - <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/> - <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/> - - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + <conditional name="input_type"> + <param name="type" type="select" label="Input Type"> + <option value="files" selected="true">Datasets</option> + <option value="collections">Collections</option> + </param> + <when value="files"> + <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </when> + <when value="collections"> + <param name="pepxml_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + <repeat name="extra_pepxml_lists" title="Additional PepXML Collections" > + <param name="extra_list" type="data_collection" multiple="true" collection_type="list" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> + </repeat> + </when> + </conditional> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="interprophet_pepxml" name="output" label="interprophet.${pepxml_files[0].display_name}" from_work_dir="interprophet_output.pep.xml"/> - </outputs> + <!-- <param name="pepxml_files" multiple="true" type="data" format="peptideprophet_pepxml" label="Peptide Prophet Results" help="These files will typically be outputs from search tools that have subsequently been run through peptide prophet"/> --> - <help> + <param name="use_nss" checked="true" type="boolean" label="Include NSS in Model" help="Include NSS (Number of Sibling Searches) in Statistical Model" truevalue="" falsevalue="--no-nss"/> + <param name="use_nrs" checked="true" type="boolean" label="Include NRS in Model" help="Include NRS (Number of Replicate Spectra) in Statistical Model" truevalue="" falsevalue="--no-nrs"/> + <param name="use_nse" checked="true" type="boolean" label="Include NSE in Model" help="Include NSE (Number of Sibling Experiments) in Statistical Model" truevalue="" falsevalue="--no-nse"/> + <param name="use_nsi" checked="true" type="boolean" label="Include NSI in Model" help="Include NSI (Number of Sibling Ions) in Statistical Model" truevalue="" falsevalue="--no-nsi"/> + <param name="use_nsm" checked="true" type="boolean" label="Include NSM in Model" help="Include NSM (Number of Sibling Modifications) in Statistical Model" truevalue="" falsevalue="--no-nsm"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + + </inputs> + <outputs> + <data format="interprophet_pepxml" name="output" from_work_dir="interprophet_output.pep.xml"/> + </outputs> + <help> **What it does** @@ -67,6 +79,5 @@ Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). - </help> - + </help> </tool>
--- a/peptide_prophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/peptide_prophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,76 +1,70 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> +<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1"> + <description>Calculate Peptide Prophet statistics on search results</description> <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Calculate Peptide Prophet statistics on search results</description> - - <command> - peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> + <command> + peptide_prophet.rb + --galaxy $input_file + -o peptide_prophet_output.pep.xml + -r + $glyco + $useicat + $phospho + $usepi + $usert + $accurate_mass + $no_ntt + $no_nmc + $use_gamma + $use_only_expect + $force_fit + $allow_alt_instruments + $maldi + $usedecoys + --decoy-prefix $decoy_prefix_string - -r - $glyco - $useicat - $phospho - $usepi - $usert - $accurate_mass - $no_ntt - $no_nmc - $use_gamma - $use_only_expect - $force_fit - $allow_alt_instruments - $maldi - $usedecoys - --decoy-prefix $decoy_prefix_string - -#if $experiment_label - --experiment-label $experiment_label -#end if - - --p-thresh $p_thresh + #if $experiment_label + --experiment-label $experiment_label + #end if - --threads $threads + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" - </command> - <inputs> - - <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> + </command> + <inputs> + <param name="input_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> - <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> - <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> - <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> - <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> - <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> - <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> - <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> - <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> - <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> - <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. - Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> - <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> - <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> - <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> - <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> - <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> - <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> - </outputs> - -<help> + <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> + <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> + <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> + <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> + <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> + <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> + <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> + <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> + <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> + <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. + Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> + <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> + <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> + <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> + <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> + <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> + <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + </inputs> + <outputs> + <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> + </outputs> + <help> **What it does** -Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. From a practical perspective it estimates the probability that each peptide assignment is correct (providing probabilities as outputs), given raw scores (possibly on some arbitrary scale) as inputs. +Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. ---- @@ -81,7 +75,7 @@ Keller A., et al. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search” *Anal. Chem.* 74, 5383-5392 (2002). -</help> + </help> <!--PeptideProphet options [following the 'O']:
--- a/pepxml_to_table.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/pepxml_to_table.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,31 +1,30 @@ -<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.0.1"> - - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> - </requirements> - - - - <description>Converts a pepXML file to a tab delimited text file</description> - - -<!-- Note .. the input file is assumed to be the first argument --> -<command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> - - -<inputs> - - <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> - <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> - -</inputs> -<outputs> - <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> -</outputs> - +<tool id="pepxml_to_table_1" name="PepXML to Table" version="1.1.1"> + <description>Converts a pepXML file to a tab delimited text file</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <!-- Note .. the input file is assumed to be the first argument --> + <command>pepxml_to_table.rb $input_file -o $output $invert_probs</command> + <inputs> + <param name="input_file" type="data" format="pepxml,raw_pepxml,peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Input File" help="A pepXML file"/> + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> + </inputs> + <outputs> + <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" format="raw_pepxml"/> + <output name="output" format="csv"> + <assert_contents> + <has_text text="ANTNNYAPKSSR" /> + </assert_contents> + </output> + </test> + </tests> <help> - Convert a pepXML file to Tab delimited text + Convert a pepXML file to Tab delimited text </help> - </tool>
--- a/protein_prophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/protein_prophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,79 +1,73 @@ -<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> - <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Calculate Protein Prophet statistics on search results</description> - +<tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.1.1"> + <description>Calculate Protein Prophet statistics on search results</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> + </requirements> -<!-- Note .. the input file is assumed to be the first argument --> - <command> - protein_prophet.rb - - --galaxy $input_file - - -o protein_prophet_results.prot.xml - - -r + <command> + protein_prophet.rb + --galaxy + + #for $input_file in $input_files: + ${input_file} + #end for + + -o protein_prophet_results.prot.xml + -r - $iproph - $nooccam - $groupwts - $normprotlen - $logprobs - $confem - $allpeps - $unmapped - $instances - $delude - - --minprob=$minprob - --minindep=$minindep - </command> - <inputs> - - <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> + $iproph + $nooccam + $groupwts + $normprotlen + $logprobs + $confem + $allpeps + $unmapped + $instances + $delude + --minprob=$minprob + --minindep=$minindep + </command> + <inputs> + <param name="input_files" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="true" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> - <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> - <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> - <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> - <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> - <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/> - <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/> - <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/> - <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/> - <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/> - <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/> + <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> + <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> + <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> + <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> + <param name="logprobs" type="boolean" label="Use the log of probability in the confidence calculations" truevalue="--log-prob" falsevalue=""/> + <param name="confem" type="boolean" label="Use the EM to compute probability given the confidenct" truevalue="--confem" falsevalue=""/> + <param name="allpeps" type="boolean" label="Consider all possible peptides in the database in the confidence model" truevalue="--allpeps" falsevalue=""/> + <param name="unmapped" type="boolean" label="Report results for unmapped proteins" truevalue="--unmapped" falsevalue=""/> + <param name="instances" type="boolean" label="Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment" truevalue="--instances" falsevalue=""/> + <param name="delude" type="boolean" label="Do NOT use peptide degeneracy information when assessing proteins" truevalue="--delude" falsevalue=""/> - <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/> - <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/> - - </inputs> - <outputs> - <data format="protxml" name="output" metadata_source="input_file" label="protein_prophet.${input_file.display_name}.protXML" from_work_dir="protein_prophet_results.prot.xml"/> - </outputs> + <param name="minprob" type="text" label="Minimum peptide prophet probability for peptides to be considered" value="0.05"/> + <param name="minindep" type="text" label="Minimum percentage of independent peptides required for a protein" value="0"/> + </inputs> + <outputs> + <data format="protxml" name="output" from_work_dir="protein_prophet_results.prot.xml"/> + </outputs> <!--NOPLOT: do not generate plot png file - NOOCCAM: non-conservative maximum protein list - GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) - NORMPROTLEN: Normalize NSP using Protein Length - LOGPROBS: Use the log of the probabilities in the Confidence calculations - CONFEM: Use the EM to compute probability given the confidence - ALLPEPS: Consider all possible peptides in the database in the confidence model - UNMAPPED: Report results for UNMAPPED proteins - INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment - DELUDE: do NOT use peptide degeneracy information when assessing proteins - - MINPROB: peptideProphet probabilty threshold (default=0.05) - MININDEP: minimum percentage of independent peptides required for a protein (default=0) - - + NOOCCAM: non-conservative maximum protein list + GROUPWTS: check peptide's total weight in the Protein Group against the threshold (default: check peptide's actual weight against threshold) + NORMPROTLEN: Normalize NSP using Protein Length + LOGPROBS: Use the log of the probabilities in the Confidence calculations + CONFEM: Use the EM to compute probability given the confidence + ALLPEPS: Consider all possible peptides in the database in the confidence model + UNMAPPED: Report results for UNMAPPED proteins + INSTANCES: Use Expected Number of Ion Instances to adjust the peptide probabilities prior to NSP adjustment + DELUDE: do NOT use peptide degeneracy information when assessing proteins + + MINPROB: peptideProphet probabilty threshold (default=0.05) + MININDEP: minimum percentage of independent peptides required for a protein (default=0) --> - <help> + <help> **What it does** @@ -88,6 +82,5 @@ Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003). - </help> - + </help> </tool>
--- a/protxml_to_table.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/protxml_to_table.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,37 +1,37 @@ -<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.0.1"> - <requirements> - <container type="docker">simonalpha/protk:1.4.0</container> - <requirement type="package" version="1.3">protk</requirement> - </requirements> - - <description>Converts a ProtXML file to a table</description> - - <command> - protxml_to_table.rb - $invert_probs - - $input_file - -o $output - </command> - - <inputs> - - <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> - <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> - </inputs> - - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - - <help> - +<tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1"> + <description>Converts a ProtXML file to a table</description> + <requirements> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> + </requirements> + <command> + protxml_to_table.rb + $invert_probs + $input_file + -o $output + </command> + <inputs> + <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/> + <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <tests> + <!-- Just test that the tool runs and produces vaguely correct output --> + <test> + <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/> + <output name="output" format="tabular"> + <assert_contents> + <has_text text="AVQKYLTAHEQSK" /> + </assert_contents> + </output> + </test> + </tests> + <help> **What it does** Converts a ProtXML file to a tab separated table - </help> - + </help> </tool>
--- a/repository_dependencies.xml Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -<?xml version="1.0"?> -<repositories description="Proteomics datatypes"> - <repository changeset_revision="9cfabf0b942d" name="proteomics_datatypes" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,1651 @@ +<?xml version="1.0" encoding="UTF-8"?> +<?xml-stylesheet type="text/xsl" href="pepXML_std.xsl"?> +<msms_pipeline_analysis date="2014-06-22T13:57:05" summary_xml="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml" xmlns="http://regis-web.systemsbiology.net/pepXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"> + <msms_run_summary base_name="mr176-BSA100fmole_BA3_01_8168.d_tandem" search_engine="X! Tandem" raw_data_type="raw" raw_data=".?"> + <sample_enzyme name="trypsin"> +<specificity cut="KR" no_cut="P" sense="C"/> +</sample_enzyme> +<search_summary base_name="mr176-BSA100fmole_BA3_01_8168.d_tandem" search_engine="X! Tandem" precursor_mass_type="monoisotopic" fragment_mass_type="monoisotopic" search_id="1"> + <search_database local_path="/Users/icooke/Desktop/iptest/AASequences.fasta" type="AA"/> + <enzymatic_search_constraint enzyme="trypsin" max_num_internal_cleavages="2" min_number_termini="1" /> + <aminoacid_modification aminoacid="E" massdiff="-18.0106" mass="111.0320" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + <aminoacid_modification aminoacid="M" massdiff="15.9949" mass="147.0354" variable="Y" /> + <aminoacid_modification aminoacid="Q" massdiff="-17.0265" mass="111.0321" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + <terminal_modification terminus="n" massdiff="42.0106" mass="43.0184" protein_terminus="N" variable="Y" symbol="^" /><!--X! Tandem n-terminal AA variable modification--> + + <!-- Input parameters --> + <parameter name="list path, default parameters" value="/Users/icooke/.rvm/gems/ruby-2.0.0-p353/gems/protk-1.2.6.pre6/lib/protk/data/tandem_isb_native_defaults.xml"/> + <parameter name="list path, taxonomy information" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem.taxonomy.xml"/> + <parameter name="output, histogram column width" value="30"/> + <parameter name="output, histograms" value="no"/> + <parameter name="output, log path" value=""/> + <parameter name="output, maximum valid expectation value" value="0.1"/> + <parameter name="output, message" value="1234567890"/> + <parameter name="output, one sequence copy" value="no"/> + <parameter name="output, parameters" value="yes"/> + <parameter name="output, path" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem"/> + <parameter name="output, path hashing" value="no"/> + <parameter name="output, performance" value="yes"/> + <parameter name="output, proteins" value="yes"/> + <parameter name="output, results" value="all"/> + <parameter name="output, sequence path" value=""/> + <parameter name="output, sequences" value="no"/> + <parameter name="output, sort results by" value="spectrum"/> + <parameter name="output, spectra" value="no"/> + <parameter name="output, xsl path" value="tandem-style.xsl"/> + <parameter name="protein, C-terminal residue modification mass" value=""/> + <parameter name="protein, N-terminal residue modification mass" value=""/> + <parameter name="protein, cleavage C-terminal mass change" value=""/> + <parameter name="protein, cleavage N-terminal mass change" value=""/> + <parameter name="protein, cleavage semi" value="yes"/> + <parameter name="protein, cleavage site" value="[RK]|{P}"/> + <parameter name="protein, homolog management" value="no"/> + <parameter name="protein, modified residue mass file" value=""/> + <parameter name="protein, quick acetyl" value="yes"/> + <parameter name="protein, taxon" value="AASequences.fasta"/> + <parameter name="refine" value="no"/> + <parameter name="refine, maximum valid expectation value" value="0.1"/> + <parameter name="refine, sequence path" value=""/> + <parameter name="refine, spectrum synthesis" value="yes"/> + <parameter name="residue, modification mass" value=""/> + <parameter name="residue, potential modification mass" value="15.994915@M"/> + <parameter name="residue, potential modification motif" value=""/> + <parameter name="scoring, a ions" value="no"/> + <parameter name="scoring, b ions" value="yes"/> + <parameter name="scoring, c ions" value="no"/> + <parameter name="scoring, cyclic permutation" value="no"/> + <parameter name="scoring, include reverse" value="no"/> + <parameter name="scoring, maximum missed cleavage sites" value="2"/> + <parameter name="scoring, minimum ion count" value="4"/> + <parameter name="scoring, x ions" value="no"/> + <parameter name="scoring, y ions" value="yes"/> + <parameter name="scoring, z ions" value="no"/> + <parameter name="spectrum, dynamic range" value="100.0"/> + <parameter name="spectrum, fragment mass type" value="monoisotopic"/> + <parameter name="spectrum, fragment monoisotopic mass error" value="0.4"/> + <parameter name="spectrum, fragment monoisotopic mass error units" value="Daltons"/> + <parameter name="spectrum, maximum parent charge" value="5"/> + <parameter name="spectrum, minimum fragment mz" value="50.0"/> + <parameter name="spectrum, minimum parent m+h" value="600.0"/> + <parameter name="spectrum, minimum peaks" value="6"/> + <parameter name="spectrum, parent monoisotopic mass error minus" value="100.0"/> + <parameter name="spectrum, parent monoisotopic mass error plus" value="100.0"/> + <parameter name="spectrum, parent monoisotopic mass error units" value="Daltons"/> + <parameter name="spectrum, parent monoisotopic mass isotope error" value="no"/> + <parameter name="spectrum, path" value="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d.mgf"/> + <parameter name="spectrum, sequence batch size" value="1000"/> + <parameter name="spectrum, threads" value="1"/> + <parameter name="spectrum, total peaks" value="50"/> + <parameter name="spectrum, use conditioning" value="yes"/> + <parameter name="spectrum, use noise suppression" value="no"/> + <!-- Unused input parameters --> + <parameter name="protein, use minimal annotations" value="yes"/> + <parameter name="refine, modification mass" value=""/> + <parameter name="refine, point mutations" value="no"/> + <parameter name="refine, potential C-terminus modifications" value=""/> + <parameter name="refine, potential N-terminus modifications" value=""/> + <parameter name="refine, potential modification mass" value=""/> + <parameter name="refine, potential modification motif" value=""/> + <parameter name="refine, tic percent" value="10"/> + <parameter name="refine, unanticipated cleavage" value="no"/> + <parameter name="refine, use potential modifications for full refinement" value="no"/> + <parameter name="scoring, pluggable scoring" value="no"/> + <parameter name="spectrum, maximum parent m+h" value="4000.0"/> + <!-- Performance parameters --> + <parameter name="list path, sequence source #1" value="/Users/icooke/Desktop/iptest/AASequences.fasta"/> + <parameter name="list path, sequence source description #1" value="no description"/> + <parameter name="modelling, duplicate peptide ids" value="0"/> + <parameter name="modelling, duplicate proteins" value="0"/> + <parameter name="modelling, total peptides used" value="542390"/> + <parameter name="modelling, total proteins used" value="33"/> + <parameter name="modelling, total spectra used" value="118"/> + <parameter name="process, start time" value="2014:06:22:13:57:05"/> + <parameter name="process, version" value="X! Tandem Sledgehammer (2013.09.01.1)"/> + <parameter name="quality values" value="12 10 7 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"/> + <parameter name="refining, # input models" value="0"/> + <parameter name="refining, # input spectra" value="0"/> + <parameter name="refining, # partial cleavage" value="0"/> + <parameter name="refining, # point mutations" value="0"/> + <parameter name="refining, # potential C-terminii" value="0"/> + <parameter name="refining, # potential N-terminii" value="0"/> + <parameter name="refining, # unanticipated cleavage" value="0"/> + <parameter name="timing, initial modelling total (sec)" value="0.63"/> + <parameter name="timing, initial modelling/spectrum (sec)" value="0.0053"/> + <parameter name="timing, load sequence models (sec)" value="0.00"/> + <parameter name="timing, refinement/spectrum (sec)" value="0.0000"/> + </search_summary> + + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00001.00001.2" start_scan="1" end_scan="1" precursor_neutral_mass="1442.6899" assumed_charge="2" index="1"> + <search_result> + <search_hit hit_rank="1" peptide="DLIRQQCYLFN" peptide_prev_aa="K" peptide_next_aa="H" protein="sp|Q26604|SMOX5_SCHMA" protein_descr="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="20" calc_neutral_pep_mass="1393.6817" massdiff="49.008" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="19.0"/> + <search_score name="nextscore" value="19.0"/> + <search_score name="bscore" value="3.2"/> + <search_score name="yscore" value="10.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00002.00002.3" start_scan="2" end_scan="2" precursor_neutral_mass="1248.6649" assumed_charge="3" index="2"> + <search_result> + <search_hit hit_rank="1" peptide="ANTNNYAPKSSR" peptide_prev_aa="A" peptide_next_aa="N" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="44" calc_neutral_pep_mass="1303.6267" massdiff="-54.962" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.6"/> + <search_score name="nextscore" value="20.6"/> + <search_score name="bscore" value="9.2"/> + <search_score name="yscore" value="10.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00003.00003.2" start_scan="3" end_scan="3" precursor_neutral_mass="1398.7025" assumed_charge="2" index="3"> + <search_result> + <search_hit hit_rank="1" peptide="NRAVFSLMQRR" peptide_prev_aa="W" peptide_next_aa="G" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="20" calc_neutral_pep_mass="1374.7307" massdiff="23.972" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="8" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="19.6"/> + <search_score name="nextscore" value="19.1"/> + <search_score name="bscore" value="2.7"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.32"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00004.00004.2" start_scan="4" end_scan="4" precursor_neutral_mass="921.5162" assumed_charge="2" index="4"> + <search_result> + <search_hit hit_rank="1" peptide="YLASAERA" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|O93367|TLX3_CHICK" protein_descr="T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="14" calc_neutral_pep_mass="861.4347" massdiff="60.081" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.5"/> + <search_score name="nextscore" value="18.5"/> + <search_score name="bscore" value="5.9"/> + <search_score name="yscore" value="9.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00005.00005.2" start_scan="5" end_scan="5" precursor_neutral_mass="1501.6666" assumed_charge="2" index="5"> + <search_result> + <search_hit hit_rank="1" peptide="FKTTRYLSVCER" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="22" calc_neutral_pep_mass="1483.7607" massdiff="17.906" num_tol_term="2" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="22.1"/> + <search_score name="nextscore" value="19.8"/> + <search_score name="bscore" value="10.5"/> + <search_score name="yscore" value="8.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00006.00006.3" start_scan="6" end_scan="6" precursor_neutral_mass="1748.7227" assumed_charge="3" index="6"> + <search_result> + <search_hit hit_rank="1" peptide="RQTAVGLELLAEAGNYSA" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|O88181|BARH2_RAT" protein_descr="BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="68" calc_neutral_pep_mass="1843.9427" massdiff="-95.220" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="21.5"/> + <search_score name="nextscore" value="21.1"/> + <search_score name="bscore" value="8.5"/> + <search_score name="yscore" value="9.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00007.00007.2" start_scan="7" end_scan="7" precursor_neutral_mass="1160.4761" assumed_charge="2" index="7"> + <search_result> + <search_hit hit_rank="1" peptide="EEPETEVRM" peptide_prev_aa="K" peptide_next_aa="V" protein="sp|Q01702|DLX3B_DANRE" protein_descr="Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="16" calc_neutral_pep_mass="1100.4807" massdiff="59.995" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="23.1"/> + <search_score name="nextscore" value="23.1"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="11.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.068"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00008.00008.2" start_scan="8" end_scan="8" precursor_neutral_mass="1106.5508" assumed_charge="2" index="8"> + <search_result> + <search_hit hit_rank="1" peptide="RQATSGMDLLS" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|Q22909|HM30_CAEEL" protein_descr="Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="20" calc_neutral_pep_mass="1175.5607" massdiff="-69.010" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="7" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="19.2"/> + <search_score name="nextscore" value="17.3"/> + <search_score name="bscore" value="8.8"/> + <search_score name="yscore" value="8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00009.00009.2" start_scan="9" end_scan="9" precursor_neutral_mass="1746.7706" assumed_charge="2" index="9"> + <search_result> + <search_hit hit_rank="1" peptide="EQLAQLMPPTSQLPGM" peptide_prev_aa="R" peptide_next_aa="P" protein="sp|P34663|HM23_CAEEL" protein_descr="Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="30" calc_neutral_pep_mass="1753.8377" massdiff="-7.067" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="7" mass="147.0354" /> + <mod_aminoacid_mass position="16" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="20.5"/> + <search_score name="nextscore" value="20.5"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00010.00010.3" start_scan="10" end_scan="10" precursor_neutral_mass="1746.7642" assumed_charge="3" index="10"> + <search_result> + <search_hit hit_rank="1" peptide="SGMNMGGMGGLSSLGDVSK" peptide_prev_aa="S" peptide_next_aa="S" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="72" calc_neutral_pep_mass="1813.7647" massdiff="-67.001" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="3" mass="147.0354" /> + <mod_aminoacid_mass position="5" mass="147.0354" /> + <mod_aminoacid_mass position="8" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="22.7"/> + <search_score name="nextscore" value="21.6"/> + <search_score name="bscore" value="11.1"/> + <search_score name="yscore" value="6.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00011.00011.2" start_scan="11" end_scan="11" precursor_neutral_mass="1261.6340" assumed_charge="2" index="11"> + <search_result> + <search_hit hit_rank="1" peptide="FLVDDILRRK" peptide_prev_aa="S" peptide_next_aa="H" protein="tr|O16132|O16132_HYDVU" protein_descr="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="18" calc_neutral_pep_mass="1255.7397" massdiff="5.894" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="17.7"/> + <search_score name="nextscore" value="17.0"/> + <search_score name="bscore" value="11"/> + <search_score name="yscore" value="3.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00012.00012.2" start_scan="12" end_scan="12" precursor_neutral_mass="1746.7675" assumed_charge="2" index="12"> + <search_result> + <search_hit hit_rank="1" peptide="KQNPGMDVNSPTIPPP" peptide_prev_aa="K" peptide_next_aa="G" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="30" calc_neutral_pep_mass="1672.8247" massdiff="73.943" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="17.1"/> + <search_score name="nextscore" value="16.3"/> + <search_score name="bscore" value="6.4"/> + <search_score name="yscore" value="8.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00013.00013.2" start_scan="13" end_scan="13" precursor_neutral_mass="1122.5442" assumed_charge="2" index="13"> + <search_result> + <search_hit hit_rank="1" peptide="PDPAKDPRADK" peptide_prev_aa="D" peptide_next_aa="K" protein="sp|O35767|NKX25_RAT" protein_descr="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="20" calc_neutral_pep_mass="1190.6047" massdiff="-68.061" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="25.8"/> + <search_score name="nextscore" value="24.0"/> + <search_score name="bscore" value="13.9"/> + <search_score name="yscore" value="12"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.035"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00014.00014.3" start_scan="14" end_scan="14" precursor_neutral_mass="1900.9309" assumed_charge="3" index="14"> + <search_result> + <search_hit hit_rank="1" peptide="ADVESAKKLGPSGQMDIV" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P52955|LBX1_MOUSE" protein_descr="Transcription factor LBX1 OS=Mus musculus GN=Lbx1 PE=1 SV=2" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="68" calc_neutral_pep_mass="1825.9247" massdiff="75.006" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="27.4"/> + <search_score name="nextscore" value="22.0"/> + <search_score name="bscore" value="9.7"/> + <search_score name="yscore" value="11.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.15"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00015.00015.2" start_scan="15" end_scan="15" precursor_neutral_mass="1106.5432" assumed_charge="2" index="15"> + <search_result> + <search_hit hit_rank="1" peptide="KLNLSATQVK" peptide_prev_aa="Q" peptide_next_aa="I" protein="sp|P22711|TIN_DROME" protein_descr="Muscle-specific homeobox protein tinman OS=Drosophila melanogaster GN=tin PE=2 SV=2" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="18" calc_neutral_pep_mass="1082.6447" massdiff="23.898" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="23.0"/> + <search_score name="nextscore" value="19.1"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="8.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.17"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00016.00016.3" start_scan="16" end_scan="16" precursor_neutral_mass="1747.7361" assumed_charge="3" index="16"> + <search_result> + <search_hit hit_rank="1" peptide="ERAELAAQLGLTQTQVK" peptide_prev_aa="P" peptide_next_aa="I" protein="sp|Q01702|DLX3B_DANRE" protein_descr="Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="64" calc_neutral_pep_mass="1837.0057" massdiff="-89.270" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="24.8"/> + <search_score name="nextscore" value="23.8"/> + <search_score name="bscore" value="9.7"/> + <search_score name="yscore" value="7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00017.00017.1" start_scan="17" end_scan="17" precursor_neutral_mass="560.2519" assumed_charge="1" index="17"> + <search_result> + <search_hit hit_rank="1" peptide="NSASATG" peptide_prev_aa="R" peptide_next_aa="W" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="12" calc_neutral_pep_mass="588.2507" massdiff="-27.999" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="12.4"/> + <search_score name="nextscore" value="11.3"/> + <search_score name="bscore" value="5.5"/> + <search_score name="yscore" value="4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00018.00018.2" start_scan="18" end_scan="18" precursor_neutral_mass="1102.4914" assumed_charge="2" index="18"> + <search_result> + <search_hit hit_rank="1" peptide="QMLLGVSARK" peptide_prev_aa="L" peptide_next_aa="H" protein="sp|P26797|HM19_CAEEL" protein_descr="Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="18" calc_neutral_pep_mass="1082.5907" massdiff="19.901" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="1" mass="111.0321" /> + <mod_aminoacid_mass position="2" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="19.2"/> + <search_score name="nextscore" value="19.2"/> + <search_score name="bscore" value="4.5"/> + <search_score name="yscore" value="10.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.9"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00019.00019.2" start_scan="19" end_scan="19" precursor_neutral_mass="1553.7028" assumed_charge="2" index="19"> + <search_result> + <search_hit hit_rank="1" peptide="ARTTFSGKQVFELE" peptide_prev_aa="K" peptide_next_aa="K" protein="sp|P56407|HM09_CAEEL" protein_descr="Homeobox protein ceh-9 OS=Caenorhabditis elegans GN=ceh-9 PE=4 SV=2" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="26" calc_neutral_pep_mass="1593.8147" massdiff="-40.112" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="17.4"/> + <search_score name="nextscore" value="17.0"/> + <search_score name="bscore" value="8.1"/> + <search_score name="yscore" value="6.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00020.00020.3" start_scan="20" end_scan="20" precursor_neutral_mass="1553.7040" assumed_charge="3" index="20"> + <search_result> + <search_hit hit_rank="1" peptide="TANNGAFTDPSSGDR" peptide_prev_aa="E" peptide_next_aa="L" protein="sp|O93590|ZAX_XENLA" protein_descr="Homeobox protein zampogna OS=Xenopus laevis GN=zax PE=2 SV=1" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="56" calc_neutral_pep_mass="1490.6387" massdiff="63.065" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="26.1"/> + <search_score name="nextscore" value="24.9"/> + <search_score name="bscore" value="8.4"/> + <search_score name="yscore" value="12"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00021.00021.2" start_scan="21" end_scan="21" precursor_neutral_mass="926.5199" assumed_charge="2" index="21"> + <search_result> + <search_hit hit_rank="1" peptide="ETEMEMK" peptide_prev_aa="E" peptide_next_aa="S" protein="tr|O77024|O77024_EPHMU" protein_descr="EmH-3 (Fragment) OS=Ephydatia muelleri GN=EmH-3 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="12" calc_neutral_pep_mass="892.3307" massdiff="34.189" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="1" mass="111.0320" /> + <mod_aminoacid_mass position="4" mass="147.0354" /> + <mod_aminoacid_mass position="6" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="17.9"/> + <search_score name="nextscore" value="16.4"/> + <search_score name="bscore" value="7.5"/> + <search_score name="yscore" value="8.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00022.00022.3" start_scan="22" end_scan="22" precursor_neutral_mass="1777.8744" assumed_charge="3" index="22"> + <search_result> + <search_hit hit_rank="1" peptide="EEPETEVRMVNGKPKK" peptide_prev_aa="K" peptide_next_aa="I" protein="sp|Q01702|DLX3B_DANRE" protein_descr="Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="60" calc_neutral_pep_mass="1867.9457" massdiff="-90.071" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="9" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="24.3"/> + <search_score name="nextscore" value="22.0"/> + <search_score name="bscore" value="6.9"/> + <search_score name="yscore" value="10.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00023.00023.1" start_scan="23" end_scan="23" precursor_neutral_mass="926.5111" assumed_charge="1" index="23"> + <search_result> + <search_hit hit_rank="1" peptide="MDTHLPF" peptide_prev_aa="-" peptide_next_aa="Q" protein="sp|P34663|HM23_CAEEL" protein_descr="Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="12" calc_neutral_pep_mass="883.3897" massdiff="43.121" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info mod_nterm_mass="43.0184" /> + <search_score name="hyperscore" value="17.2"/> + <search_score name="nextscore" value="15.8"/> + <search_score name="bscore" value="12.5"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00024.00024.2" start_scan="24" end_scan="24" precursor_neutral_mass="1304.7563" assumed_charge="2" index="24"> + <search_result> + <search_hit hit_rank="1" peptide="QDQTLELLGPPP" peptide_prev_aa="R" peptide_next_aa="P" protein="sp|O35767|NKX25_RAT" protein_descr="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="22" calc_neutral_pep_mass="1271.6397" massdiff="33.117" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="1" mass="111.0321" /> + </modification_info> + <search_score name="hyperscore" value="22.1"/> + <search_score name="nextscore" value="21.7"/> + <search_score name="bscore" value="10"/> + <search_score name="yscore" value="8.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.45"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00025.00025.2" start_scan="25" end_scan="25" precursor_neutral_mass="1289.7434" assumed_charge="2" index="25"> + <search_result> + <search_hit hit_rank="1" peptide="IAQLLKKHKPGAG" peptide_prev_aa="K" peptide_next_aa="G" protein="tr|Q9YHC2|Q9YHC2_CHICK" protein_descr="Homeodomain protein (Fragment) OS=Gallus gallus GN=Nkx-6.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="24" calc_neutral_pep_mass="1341.8247" massdiff="-52.081" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="22.3"/> + <search_score name="nextscore" value="19.8"/> + <search_score name="bscore" value="7.1"/> + <search_score name="yscore" value="9.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00026.00026.2" start_scan="26" end_scan="26" precursor_neutral_mass="1319.7180" assumed_charge="2" index="26"> + <search_result> + <search_hit hit_rank="1" peptide="PTVNGEIDEFGR" peptide_prev_aa="L" peptide_next_aa="C" protein="sp|P56407|HM09_CAEEL" protein_descr="Homeobox protein ceh-9 OS=Caenorhabditis elegans GN=ceh-9 PE=4 SV=2" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1314.6207" massdiff="5.097" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="22.6"/> + <search_score name="nextscore" value="21.9"/> + <search_score name="bscore" value="8"/> + <search_score name="yscore" value="10.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00027.00027.2" start_scan="27" end_scan="27" precursor_neutral_mass="1123.5366" assumed_charge="2" index="27"> + <search_result> + <search_hit hit_rank="1" peptide="CKKQTIESR" peptide_prev_aa="K" peptide_next_aa="T" protein="tr|O16132|O16132_HYDVU" protein_descr="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="16" calc_neutral_pep_mass="1073.5647" massdiff="49.972" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="18.9"/> + <search_score name="nextscore" value="17.6"/> + <search_score name="bscore" value="8.3"/> + <search_score name="yscore" value="9.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00028.00028.2" start_scan="28" end_scan="28" precursor_neutral_mass="1348.7433" assumed_charge="2" index="28"> + <search_result> + <search_hit hit_rank="1" peptide="PENLLLHGPFSR" peptide_prev_aa="S" peptide_next_aa="K" protein="tr|Q90263|Q90263_DANRE" protein_descr="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1360.7247" massdiff="-11.981" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="20.1"/> + <search_score name="nextscore" value="18.0"/> + <search_score name="bscore" value="11.1"/> + <search_score name="yscore" value="8.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00029.00029.2" start_scan="29" end_scan="29" precursor_neutral_mass="1122.5332" assumed_charge="2" index="29"> + <search_result> + <search_hit hit_rank="1" peptide="ERLFQETR" peptide_prev_aa="L" peptide_next_aa="Y" protein="tr|O70238|O70238_MOUSE" protein_descr="Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="14" calc_neutral_pep_mass="1059.5457" massdiff="62.988" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="19.8"/> + <search_score name="nextscore" value="19.8"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="8.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00030.00030.2" start_scan="30" end_scan="30" precursor_neutral_mass="1186.6753" assumed_charge="2" index="30"> + <search_result> + <search_hit hit_rank="1" peptide="SPNLPFSATIPR" peptide_prev_aa="L" peptide_next_aa="V" protein="sp|P34663|HM23_CAEEL" protein_descr="Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="22" calc_neutral_pep_mass="1280.6877" massdiff="-94.012" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="24.1"/> + <search_score name="nextscore" value="20.7"/> + <search_score name="bscore" value="7.9"/> + <search_score name="yscore" value="11.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.38"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00031.00031.1" start_scan="31" end_scan="31" precursor_neutral_mass="650.3617" assumed_charge="1" index="31"> + <search_result> + <search_hit hit_rank="1" peptide="ILPSSLK" peptide_prev_aa="N" peptide_next_aa="H" protein="sp|Q26604|SMOX5_SCHMA" protein_descr="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="12" calc_neutral_pep_mass="738.4637" massdiff="-88.102" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="15.5"/> + <search_score name="nextscore" value="14.3"/> + <search_score name="bscore" value="12.4"/> + <search_score name="yscore" value="3.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00032.00032.2" start_scan="32" end_scan="32" precursor_neutral_mass="926.5107" assumed_charge="2" index="32"> + <search_result> + <search_hit hit_rank="1" peptide="DEDQIQV" peptide_prev_aa="D" peptide_next_aa="-" protein="sp|Q24255|BARH1_DROME" protein_descr="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="12" calc_neutral_pep_mass="827.3657" massdiff="99.145" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="16.8"/> + <search_score name="nextscore" value="16.7"/> + <search_score name="bscore" value="8.7"/> + <search_score name="yscore" value="10.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00033.00033.3" start_scan="33" end_scan="33" precursor_neutral_mass="1438.8547" assumed_charge="3" index="33"> + <search_result> + <search_hit hit_rank="1" peptide="CPPRAPSPPPCTLR" peptide_prev_aa="S" peptide_next_aa="K" protein="sp|P70354|MSX3_MOUSE" protein_descr="Homeobox protein MSX-3 OS=Mus musculus GN=Msx3 PE=1 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="52" calc_neutral_pep_mass="1472.7377" massdiff="-33.883" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.1"/> + <search_score name="nextscore" value="19.4"/> + <search_score name="bscore" value="5.5"/> + <search_score name="yscore" value="10.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00034.00034.2" start_scan="34" end_scan="34" precursor_neutral_mass="1304.7497" assumed_charge="2" index="34"> + <search_result> + <search_hit hit_rank="1" peptide="PENLLLHGPFSR" peptide_prev_aa="S" peptide_next_aa="K" protein="tr|Q90263|Q90263_DANRE" protein_descr="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1360.7247" massdiff="-55.975" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.3"/> + <search_score name="nextscore" value="16.9"/> + <search_score name="bscore" value="10.3"/> + <search_score name="yscore" value="7.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00035.00035.1" start_scan="35" end_scan="35" precursor_neutral_mass="650.3643" assumed_charge="1" index="35"> + <search_result> + <search_hit hit_rank="1" peptide="LLDPQN" peptide_prev_aa="R" peptide_next_aa="K" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="10" calc_neutral_pep_mass="680.3497" massdiff="-29.985" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="17.0"/> + <search_score name="nextscore" value="15.1"/> + <search_score name="bscore" value="11.6"/> + <search_score name="yscore" value="11.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.64"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00036.00036.1" start_scan="36" end_scan="36" precursor_neutral_mass="650.3623" assumed_charge="1" index="36"> + <search_result> + <search_hit hit_rank="1" peptide="ILWGSH" peptide_prev_aa="R" peptide_next_aa="V" protein="tr|O35455|O35455_MOUSE" protein_descr="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="10" calc_neutral_pep_mass="693.3597" massdiff="-42.997" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="14.5"/> + <search_score name="nextscore" value="13.5"/> + <search_score name="bscore" value="9.2"/> + <search_score name="yscore" value="8.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00037.00037.2" start_scan="37" end_scan="37" precursor_neutral_mass="1141.7448" assumed_charge="2" index="37"> + <search_result> + <search_hit hit_rank="1" peptide="SLAAGDLSARL" peptide_prev_aa="R" peptide_next_aa="E" protein="sp|O35767|NKX25_RAT" protein_descr="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="20" calc_neutral_pep_mass="1054.5767" massdiff="87.168" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="25.9"/> + <search_score name="nextscore" value="24.7"/> + <search_score name="bscore" value="11.3"/> + <search_score name="yscore" value="10.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00038.00038.2" start_scan="38" end_scan="38" precursor_neutral_mass="1575.8289" assumed_charge="2" index="38"> + <search_result> + <search_hit hit_rank="1" peptide="TQPPSISNILPSSLK" peptide_prev_aa="L" peptide_next_aa="H" protein="sp|Q26604|SMOX5_SCHMA" protein_descr="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="28" calc_neutral_pep_mass="1562.8667" massdiff="12.962" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="27.1"/> + <search_score name="nextscore" value="21.0"/> + <search_score name="bscore" value="2.1"/> + <search_score name="yscore" value="12.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.15"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00039.00039.3" start_scan="39" end_scan="39" precursor_neutral_mass="1620.9787" assumed_charge="3" index="39"> + <search_result> + <search_hit hit_rank="1" peptide="QKGGSSDHASDEEDD" peptide_prev_aa="K" peptide_next_aa="D" protein="sp|Q18273|HM43_CAEEL" protein_descr="Homeobox protein ceh-43 OS=Caenorhabditis elegans GN=ceh-43 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="56" calc_neutral_pep_mass="1557.5817" massdiff="63.397" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="26.3"/> + <search_score name="nextscore" value="23.3"/> + <search_score name="bscore" value="9.1"/> + <search_score name="yscore" value="11.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.43"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00040.00040.3" start_scan="40" end_scan="40" precursor_neutral_mass="1638.9916" assumed_charge="3" index="40"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMGGL" peptide_prev_aa="R" peptide_next_aa="S" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="14" tot_num_ions="60" calc_neutral_pep_mass="1557.6087" massdiff="81.383" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="8" mass="147.0354" /> + <mod_aminoacid_mass position="13" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="28.4"/> + <search_score name="nextscore" value="25.1"/> + <search_score name="bscore" value="6.8"/> + <search_score name="yscore" value="8.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00041.00041.2" start_scan="41" end_scan="41" precursor_neutral_mass="1638.9911" assumed_charge="2" index="41"> + <search_result> + <search_hit hit_rank="1" peptide="LPSLPSLADDGTRLSA" peptide_prev_aa="R" peptide_next_aa="H" protein="tr|Q90853|Q90853_CHICK" protein_descr="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="30" calc_neutral_pep_mass="1593.8367" massdiff="45.154" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="15.6"/> + <search_score name="nextscore" value="15.4"/> + <search_score name="bscore" value="9.9"/> + <search_score name="yscore" value="6.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.6"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00042.00042.1" start_scan="42" end_scan="42" precursor_neutral_mass="650.3651" assumed_charge="1" index="42"> + <search_result> + <search_hit hit_rank="1" peptide="EHTTTK" peptide_prev_aa="P" peptide_next_aa="I" protein="sp|Q18273|HM43_CAEEL" protein_descr="Homeobox protein ceh-43 OS=Caenorhabditis elegans GN=ceh-43 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="10" calc_neutral_pep_mass="697.3397" massdiff="-46.975" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="9.8"/> + <search_score name="nextscore" value="8.0"/> + <search_score name="bscore" value="5.8"/> + <search_score name="yscore" value="5.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="28"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00043.00043.2" start_scan="43" end_scan="43" precursor_neutral_mass="1304.7553" assumed_charge="2" index="43"> + <search_result> + <search_hit hit_rank="1" peptide="MEPAAGAQGPHQ" peptide_prev_aa="-" peptide_next_aa="H" protein="sp|O93367|TLX3_CHICK" protein_descr="T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="22" calc_neutral_pep_mass="1216.5297" massdiff="88.226" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info mod_nterm_mass="43.0184" /> + <search_score name="hyperscore" value="21.5"/> + <search_score name="nextscore" value="20.9"/> + <search_score name="bscore" value="6.7"/> + <search_score name="yscore" value="9.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00044.00044.2" start_scan="44" end_scan="44" precursor_neutral_mass="1282.7467" assumed_charge="2" index="44"> + <search_result> + <search_hit hit_rank="1" peptide="ARTVFSDPQLSGL" peptide_prev_aa="K" peptide_next_aa="E" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="24" calc_neutral_pep_mass="1371.7147" massdiff="-88.968" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.4"/> + <search_score name="nextscore" value="19.5"/> + <search_score name="bscore" value="7.4"/> + <search_score name="yscore" value="8.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00045.00045.3" start_scan="45" end_scan="45" precursor_neutral_mass="1879.9879" assumed_charge="3" index="45"> + <search_result> + <search_hit hit_rank="1" peptide="VGMEGSNLGAPLSAYRQS" peptide_prev_aa="K" peptide_next_aa="Q" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="68" calc_neutral_pep_mass="1817.8727" massdiff="62.115" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="24.2"/> + <search_score name="nextscore" value="22.9"/> + <search_score name="bscore" value="8.2"/> + <search_score name="yscore" value="9.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.7"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00046.00046.2" start_scan="46" end_scan="46" precursor_neutral_mass="1418.7402" assumed_charge="2" index="46"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMGG" peptide_prev_aa="R" peptide_next_aa="L" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="28" calc_neutral_pep_mass="1460.5197" massdiff="-41.780" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="2" mass="147.0354" /> + <mod_aminoacid_mass position="10" mass="147.0354" /> + <mod_aminoacid_mass position="13" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="24.8"/> + <search_score name="nextscore" value="24.7"/> + <search_score name="bscore" value="6.4"/> + <search_score name="yscore" value="9.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.56"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00047.00047.3" start_scan="47" end_scan="47" precursor_neutral_mass="1418.7405" assumed_charge="3" index="47"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMGG" peptide_prev_aa="R" peptide_next_aa="L" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="11" tot_num_ions="56" calc_neutral_pep_mass="1476.5137" massdiff="-57.773" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="2" mass="147.0354" /> + <mod_aminoacid_mass position="8" mass="147.0354" /> + <mod_aminoacid_mass position="10" mass="147.0354" /> + <mod_aminoacid_mass position="13" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="22.9"/> + <search_score name="nextscore" value="22.4"/> + <search_score name="bscore" value="7.6"/> + <search_score name="yscore" value="9.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00048.00048.2" start_scan="48" end_scan="48" precursor_neutral_mass="1466.7865" assumed_charge="2" index="48"> + <search_result> + <search_hit hit_rank="1" peptide="SDIDDPSSETDSK" peptide_prev_aa="G" peptide_next_aa="K" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="24" calc_neutral_pep_mass="1376.5577" massdiff="90.229" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="23.7"/> + <search_score name="nextscore" value="23.3"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="12.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.098"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00049.00049.2" start_scan="49" end_scan="49" precursor_neutral_mass="1332.7450" assumed_charge="2" index="49"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMG" peptide_prev_aa="R" peptide_next_aa="G" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="26" calc_neutral_pep_mass="1387.5027" massdiff="-54.758" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="8" mass="147.0354" /> + <mod_aminoacid_mass position="10" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="17.6"/> + <search_score name="nextscore" value="17.6"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00050.00050.2" start_scan="50" end_scan="50" precursor_neutral_mass="1510.8827" assumed_charge="2" index="50"> + <search_result> + <search_hit hit_rank="1" peptide="AVQKYLTAHEQSK" peptide_prev_aa="F" peptide_next_aa="L" protein="tr|Q24786|Q24786_9METZ" protein_descr="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="24" calc_neutral_pep_mass="1483.7787" massdiff="27.104" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="23.7"/> + <search_score name="nextscore" value="20.7"/> + <search_score name="bscore" value="6.7"/> + <search_score name="yscore" value="8.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.52"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00051.00051.2" start_scan="51" end_scan="51" precursor_neutral_mass="1178.6636" assumed_charge="2" index="51"> + <search_result> + <search_hit hit_rank="1" peptide="MIHLTPTQVK" peptide_prev_aa="S" peptide_next_aa="I" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="18" calc_neutral_pep_mass="1148.6377" massdiff="30.026" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="21.1"/> + <search_score name="nextscore" value="20.1"/> + <search_score name="bscore" value="12.2"/> + <search_score name="yscore" value="8.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00052.00052.2" start_scan="52" end_scan="52" precursor_neutral_mass="950.5069" assumed_charge="2" index="52"> + <search_result> + <search_hit hit_rank="1" peptide="IESLLEKK" peptide_prev_aa="N" peptide_next_aa="S" protein="sp|P26797|HM19_CAEEL" protein_descr="Homeobox protein ceh-19 OS=Caenorhabditis elegans GN=ceh-19 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="14" calc_neutral_pep_mass="940.5597" massdiff="9.947" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="18.0"/> + <search_score name="nextscore" value="17.3"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00053.00053.2" start_scan="53" end_scan="53" precursor_neutral_mass="1201.6716" assumed_charge="2" index="53"> + <search_result> + <search_hit hit_rank="1" peptide="LSSPGQLKAARR" peptide_prev_aa="R" peptide_next_aa="R" protein="sp|O08686|BARX2_MOUSE" protein_descr="Homeobox protein BarH-like 2 OS=Mus musculus GN=Barx2 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1264.7367" massdiff="-63.065" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.1"/> + <search_score name="nextscore" value="20.0"/> + <search_score name="bscore" value="8.2"/> + <search_score name="yscore" value="10.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00054.00054.2" start_scan="54" end_scan="54" precursor_neutral_mass="1162.6670" assumed_charge="2" index="54"> + <search_result> + <search_hit hit_rank="1" peptide="HSSGSNASTINK" peptide_prev_aa="P" peptide_next_aa="Q" protein="tr|Q24785|Q24785_9METZ" protein_descr="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1183.5577" massdiff="-20.891" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.4"/> + <search_score name="nextscore" value="18.4"/> + <search_score name="bscore" value="8.1"/> + <search_score name="yscore" value="9.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00055.00055.2" start_scan="55" end_scan="55" precursor_neutral_mass="1418.7378" assumed_charge="2" index="55"> + <search_result> + <search_hit hit_rank="1" peptide="QPLPGSDVAAFLVPT" peptide_prev_aa="R" peptide_next_aa="K" protein="tr|O35455|O35455_MOUSE" protein_descr="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="28" calc_neutral_pep_mass="1492.7927" massdiff="-74.055" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="24.2"/> + <search_score name="nextscore" value="21.8"/> + <search_score name="bscore" value="12.4"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00056.00056.3" start_scan="56" end_scan="56" precursor_neutral_mass="1418.7358" assumed_charge="3" index="56"> + <search_result> + <search_hit hit_rank="1" peptide="LVLFHRGPAGHRSG" peptide_prev_aa="R" peptide_next_aa="G" protein="tr|Q90853|Q90853_CHICK" protein_descr="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="52" calc_neutral_pep_mass="1484.8117" massdiff="-66.076" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="24.3"/> + <search_score name="nextscore" value="23.8"/> + <search_score name="bscore" value="7.6"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00057.00057.2" start_scan="57" end_scan="57" precursor_neutral_mass="1466.7853" assumed_charge="2" index="57"> + <search_result> + <search_hit hit_rank="1" peptide="SDIDDPSSETDSK" peptide_prev_aa="G" peptide_next_aa="K" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="24" calc_neutral_pep_mass="1376.5577" massdiff="90.228" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="23.9"/> + <search_score name="nextscore" value="23.5"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="12.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.25"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00058.00058.2" start_scan="58" end_scan="58" precursor_neutral_mass="1013.6479" assumed_charge="2" index="58"> + <search_result> + <search_hit hit_rank="1" peptide="TQLIALERK" peptide_prev_aa="S" peptide_next_aa="F" protein="tr|Q24785|Q24785_9METZ" protein_descr="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="16" calc_neutral_pep_mass="1052.6347" massdiff="-38.987" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="22.9"/> + <search_score name="nextscore" value="20.2"/> + <search_score name="bscore" value="11.5"/> + <search_score name="yscore" value="8.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.46"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00059.00059.2" start_scan="59" end_scan="59" precursor_neutral_mass="1356.7262" assumed_charge="2" index="59"> + <search_result> + <search_hit hit_rank="1" peptide="LVAAVAARTTQASST" peptide_prev_aa="K" peptide_next_aa="S" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="28" calc_neutral_pep_mass="1427.7737" massdiff="-71.048" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.1"/> + <search_score name="nextscore" value="18.9"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="8.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00060.00060.2" start_scan="60" end_scan="60" precursor_neutral_mass="1510.8183" assumed_charge="2" index="60"> + <search_result> + <search_hit hit_rank="1" peptide="MFQHNKKCFTIE" peptide_prev_aa="-" peptide_next_aa="S" protein="tr|Q90263|Q90263_DANRE" protein_descr="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1" num_tot_proteins="2" num_matched_ions="6" tot_num_ions="22" calc_neutral_pep_mass="1522.7057" massdiff="-11.887" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="1" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="19.8"/> + <search_score name="nextscore" value="19.8"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="8.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00061.00061.2" start_scan="61" end_scan="61" precursor_neutral_mass="1414.7370" assumed_charge="2" index="61"> + <search_result> + <search_hit hit_rank="1" peptide="LPAGGRGAGKHCPPY" peptide_prev_aa="P" peptide_next_aa="-" protein="tr|O35455|O35455_MOUSE" protein_descr="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="28" calc_neutral_pep_mass="1461.7297" massdiff="-46.993" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="21.2"/> + <search_score name="nextscore" value="20.5"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.8"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00062.00062.2" start_scan="62" end_scan="62" precursor_neutral_mass="1429.7331" assumed_charge="2" index="62"> + <search_result> + <search_hit hit_rank="1" peptide="LVAAVAARTTQASST" peptide_prev_aa="K" peptide_next_aa="S" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="28" calc_neutral_pep_mass="1427.7737" massdiff="1.959" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="26.1"/> + <search_score name="nextscore" value="22.0"/> + <search_score name="bscore" value="8.3"/> + <search_score name="yscore" value="9.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.046"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00063.00063.3" start_scan="63" end_scan="63" precursor_neutral_mass="1906.9863" assumed_charge="3" index="63"> + <search_result> + <search_hit hit_rank="1" peptide="SLNESIQPDPLCLHNSSL" peptide_prev_aa="K" peptide_next_aa="F" protein="sp|O93367|TLX3_CHICK" protein_descr="T-cell leukemia homeobox protein 3 OS=Gallus gallus GN=TLX3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="68" calc_neutral_pep_mass="1947.9357" massdiff="-40.949" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="21.9"/> + <search_score name="nextscore" value="20.9"/> + <search_score name="bscore" value="9.4"/> + <search_score name="yscore" value="12"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00064.00064.2" start_scan="64" end_scan="64" precursor_neutral_mass="1906.9855" assumed_charge="2" index="64"> + <search_result> + <search_hit hit_rank="1" peptide="DSMSILTQTPSEPNAAHP" peptide_prev_aa="K" peptide_next_aa="Q" protein="sp|Q24255|BARH1_DROME" protein_descr="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="34" calc_neutral_pep_mass="1876.8627" massdiff="30.123" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="15.9"/> + <search_score name="nextscore" value="15.8"/> + <search_score name="bscore" value="7.3"/> + <search_score name="yscore" value="12.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00065.00065.2" start_scan="65" end_scan="65" precursor_neutral_mass="1162.6667" assumed_charge="2" index="65"> + <search_result> + <search_hit hit_rank="1" peptide="HSSGSNASTINK" peptide_prev_aa="P" peptide_next_aa="Q" protein="tr|Q24785|Q24785_9METZ" protein_descr="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="22" calc_neutral_pep_mass="1183.5577" massdiff="-20.891" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.8"/> + <search_score name="nextscore" value="19.0"/> + <search_score name="bscore" value="8.2"/> + <search_score name="yscore" value="9.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00066.00066.2" start_scan="66" end_scan="66" precursor_neutral_mass="1536.8528" assumed_charge="2" index="66"> + <search_result> + <search_hit hit_rank="1" peptide="LQLKQNNAKGSGIK" peptide_prev_aa="Y" peptide_next_aa="C" protein="tr|Q23819|Q23819_HYDVD" protein_descr="Cnox3 protein (Fragment) OS=Hydra viridissima GN=cnox3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="26" calc_neutral_pep_mass="1479.8517" massdiff="57.001" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="21.7"/> + <search_score name="nextscore" value="19.3"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="10.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.29"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00067.00067.3" start_scan="67" end_scan="67" precursor_neutral_mass="2109.0833" assumed_charge="3" index="67"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMGGLSSLGD" peptide_prev_aa="R" peptide_next_aa="V" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="12" tot_num_ions="80" calc_neutral_pep_mass="2048.7947" massdiff="60.289" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="2" mass="147.0354" /> + <mod_aminoacid_mass position="8" mass="147.0354" /> + <mod_aminoacid_mass position="10" mass="147.0354" /> + <mod_aminoacid_mass position="13" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="28.4"/> + <search_score name="nextscore" value="27.1"/> + <search_score name="bscore" value="10.1"/> + <search_score name="yscore" value="5.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00068.00068.2" start_scan="68" end_scan="68" precursor_neutral_mass="1478.8432" assumed_charge="2" index="68"> + <search_result> + <search_hit hit_rank="1" peptide="FMAPSSGMNMGGMG" peptide_prev_aa="R" peptide_next_aa="G" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="26" calc_neutral_pep_mass="1387.5027" massdiff="91.341" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="8" mass="147.0354" /> + <mod_aminoacid_mass position="10" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="22.1"/> + <search_score name="nextscore" value="22.0"/> + <search_score name="bscore" value="2.6"/> + <search_score name="yscore" value="7.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00069.00069.2" start_scan="69" end_scan="69" precursor_neutral_mass="1493.8317" assumed_charge="2" index="69"> + <search_result> + <search_hit hit_rank="1" peptide="FIISANGAAVAGKQE" peptide_prev_aa="K" peptide_next_aa="Q" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="28" calc_neutral_pep_mass="1456.7677" massdiff="37.064" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="21.9"/> + <search_score name="nextscore" value="19.5"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="10.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.22"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00070.00070.2" start_scan="70" end_scan="70" precursor_neutral_mass="979.4841" assumed_charge="2" index="70"> + <search_result> + <search_hit hit_rank="1" peptide="RQTAVGLEL" peptide_prev_aa="K" peptide_next_aa="L" protein="sp|O88181|BARH2_RAT" protein_descr="BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1" num_tot_proteins="2" num_matched_ions="6" tot_num_ions="16" calc_neutral_pep_mass="967.5447" massdiff="11.939" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <alternative_protein protein="sp|Q24255|BARH1_DROME" protein_descr="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2" num_tol_term="1"/> + <search_score name="hyperscore" value="22.4"/> + <search_score name="nextscore" value="22.4"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="11"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.27"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00071.00071.2" start_scan="71" end_scan="71" precursor_neutral_mass="1110.5765" assumed_charge="2" index="71"> + <search_result> + <search_hit hit_rank="1" peptide="LPPYQDTMR" peptide_prev_aa="E" peptide_next_aa="N" protein="tr|Q9YH59|Q9YH59_CHICK" protein_descr="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="16" calc_neutral_pep_mass="1101.5277" massdiff="9.049" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.2"/> + <search_score name="nextscore" value="18.0"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="10.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00072.00072.2" start_scan="72" end_scan="72" precursor_neutral_mass="1490.8072" assumed_charge="2" index="72"> + <search_result> + <search_hit hit_rank="1" peptide="DQIANKLNLTPTQV" peptide_prev_aa="R" peptide_next_aa="K" protein="tr|O16132|O16132_HYDVU" protein_descr="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="26" calc_neutral_pep_mass="1535.8307" massdiff="-45.023" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="18.4"/> + <search_score name="nextscore" value="18.1"/> + <search_score name="bscore" value="8.8"/> + <search_score name="yscore" value="8.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00073.00073.2" start_scan="73" end_scan="73" precursor_neutral_mass="1506.8015" assumed_charge="2" index="73"> + <search_result> + <search_hit hit_rank="1" peptide="WPFAASVRKSYD" peptide_prev_aa="S" peptide_next_aa="P" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="22" calc_neutral_pep_mass="1407.6937" massdiff="99.108" num_tol_term="0" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="19.2"/> + <search_score name="nextscore" value="17.8"/> + <search_score name="bscore" value="12"/> + <search_score name="yscore" value="9.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00074.00074.2" start_scan="74" end_scan="74" precursor_neutral_mass="1162.6670" assumed_charge="2" index="74"> + <search_result> + <search_hit hit_rank="1" peptide="SKEAEIEESVR" peptide_prev_aa="R" peptide_next_aa="N" protein="tr|Q23824|Q23824_HYDVD" protein_descr="Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="20" calc_neutral_pep_mass="1257.6197" massdiff="-94.953" num_tol_term="2" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="21.2"/> + <search_score name="nextscore" value="19.4"/> + <search_score name="bscore" value="6.5"/> + <search_score name="yscore" value="9.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00075.00075.2" start_scan="75" end_scan="75" precursor_neutral_mass="1529.8090" assumed_charge="2" index="75"> + <search_result> + <search_hit hit_rank="1" peptide="IGIGTFPARTTDSISS" peptide_prev_aa="K" peptide_next_aa="N" protein="tr|Q24785|Q24785_9METZ" protein_descr="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="30" calc_neutral_pep_mass="1603.8207" massdiff="-74.012" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="18.9"/> + <search_score name="nextscore" value="18.9"/> + <search_score name="bscore" value="10.6"/> + <search_score name="yscore" value="0"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00076.00076.2" start_scan="76" end_scan="76" precursor_neutral_mass="1414.7345" assumed_charge="2" index="76"> + <search_result> + <search_hit hit_rank="1" peptide="LVAAVAARTTQASST" peptide_prev_aa="K" peptide_next_aa="S" protein="sp|P22807|SLOU_DROME" protein_descr="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="28" calc_neutral_pep_mass="1427.7737" massdiff="-13.039" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="20.3"/> + <search_score name="nextscore" value="17.6"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="8.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.1"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00077.00077.2" start_scan="77" end_scan="77" precursor_neutral_mass="1521.7961" assumed_charge="2" index="77"> + <search_result> + <search_hit hit_rank="1" peptide="EERTNNITTMAMK" peptide_prev_aa="E" peptide_next_aa="R" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="24" calc_neutral_pep_mass="1501.7017" massdiff="20.094" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="1" mass="111.0320" /> + </modification_info> + <search_score name="hyperscore" value="23.9"/> + <search_score name="nextscore" value="23.8"/> + <search_score name="bscore" value="4"/> + <search_score name="yscore" value="9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.18"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00078.00078.1" start_scan="78" end_scan="78" precursor_neutral_mass="494.2668" assumed_charge="1" index="78"> + <search_result> + <search_hit hit_rank="1" peptide="RAAAGGG" peptide_prev_aa="R" peptide_next_aa="G" protein="tr|Q90853|Q90853_CHICK" protein_descr="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="12" calc_neutral_pep_mass="540.2767" massdiff="-46.010" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="12.7"/> + <search_score name="nextscore" value="9.7"/> + <search_score name="bscore" value="10"/> + <search_score name="yscore" value="7.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="4.3"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00079.00079.2" start_scan="79" end_scan="79" precursor_neutral_mass="1478.8394" assumed_charge="2" index="79"> + <search_result> + <search_hit hit_rank="1" peptide="NLLLHGPFSRKPK" peptide_prev_aa="E" peptide_next_aa="R" protein="tr|Q90263|Q90263_DANRE" protein_descr="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="24" calc_neutral_pep_mass="1487.8727" massdiff="-9.033" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="19.4"/> + <search_score name="nextscore" value="18.9"/> + <search_score name="bscore" value="10"/> + <search_score name="yscore" value="9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.9"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00080.00080.2" start_scan="80" end_scan="80" precursor_neutral_mass="1340.7300" assumed_charge="2" index="80"> + <search_result> + <search_hit hit_rank="1" peptide="DNSSDVDIVGDAK" peptide_prev_aa="E" peptide_next_aa="L" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="24" calc_neutral_pep_mass="1315.5887" massdiff="25.141" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="18.4"/> + <search_score name="nextscore" value="18.0"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="10.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00081.00081.2" start_scan="81" end_scan="81" precursor_neutral_mass="1304.7524" assumed_charge="2" index="81"> + <search_result> + <search_hit hit_rank="1" peptide="LGHFPPTAGGNGL" peptide_prev_aa="K" peptide_next_aa="N" protein="sp|Q24255|BARH1_DROME" protein_descr="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="24" calc_neutral_pep_mass="1218.6147" massdiff="86.138" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="16.5"/> + <search_score name="nextscore" value="16.1"/> + <search_score name="bscore" value="10"/> + <search_score name="yscore" value="6.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00082.00082.2" start_scan="82" end_scan="82" precursor_neutral_mass="1955.0314" assumed_charge="2" index="82"> + <search_result> + <search_hit hit_rank="1" peptide="SYDPALRSYFSRFNNSD" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="32" calc_neutral_pep_mass="2019.9077" massdiff="-64.876" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="16.7"/> + <search_score name="nextscore" value="16.4"/> + <search_score name="bscore" value="2.8"/> + <search_score name="yscore" value="13.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00084.00084.2" start_scan="84" end_scan="84" precursor_neutral_mass="1414.7363" assumed_charge="2" index="83"> + <search_result> + <search_hit hit_rank="1" peptide="AHAHANATTPTHSK" peptide_prev_aa="D" peptide_next_aa="A" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="26" calc_neutral_pep_mass="1424.6907" massdiff="-9.954" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="20.4"/> + <search_score name="nextscore" value="19.4"/> + <search_score name="bscore" value="6.1"/> + <search_score name="yscore" value="8.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.8"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00083.00083.2" start_scan="83" end_scan="83" precursor_neutral_mass="1398.7408" assumed_charge="2" index="84"> + <search_result> + <search_hit hit_rank="1" peptide="SEPGKQPGEATSSSG" peptide_prev_aa="R" peptide_next_aa="D" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="7" tot_num_ions="28" calc_neutral_pep_mass="1399.6217" massdiff="-0.881" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="21.1"/> + <search_score name="nextscore" value="18.3"/> + <search_score name="bscore" value="2.5"/> + <search_score name="yscore" value="9.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.43"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00085.00085.2" start_scan="85" end_scan="85" precursor_neutral_mass="1535.7957" assumed_charge="2" index="85"> + <search_result> + <search_hit hit_rank="1" peptide="KHKPGAGGLLPHPAEG" peptide_prev_aa="K" peptide_next_aa="E" protein="tr|Q9YHC2|Q9YHC2_CHICK" protein_descr="Homeodomain protein (Fragment) OS=Gallus gallus GN=Nkx-6.1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="30" calc_neutral_pep_mass="1546.8367" massdiff="-11.041" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="26.5"/> + <search_score name="nextscore" value="25.4"/> + <search_score name="bscore" value="5"/> + <search_score name="yscore" value="11.6"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.12"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00086.00086.2" start_scan="86" end_scan="86" precursor_neutral_mass="1490.8037" assumed_charge="2" index="86"> + <search_result> + <search_hit hit_rank="1" peptide="AELRAELGPAPSPPK" peptide_prev_aa="L" peptide_next_aa="C" protein="sp|O35767|NKX25_RAT" protein_descr="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="28" calc_neutral_pep_mass="1513.8257" massdiff="-23.022" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="18.2"/> + <search_score name="nextscore" value="18.2"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00087.00087.2" start_scan="87" end_scan="87" precursor_neutral_mass="1755.8887" assumed_charge="2" index="87"> + <search_result> + <search_hit hit_rank="1" peptide="ALPTTLAMRAAAPAPAPAP" peptide_prev_aa="R" peptide_next_aa="G" protein="tr|O35455|O35455_MOUSE" protein_descr="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="36" calc_neutral_pep_mass="1768.9657" massdiff="-13.077" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="22.9"/> + <search_score name="nextscore" value="16.4"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="11.5"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.075"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00088.00088.2" start_scan="88" end_scan="88" precursor_neutral_mass="1739.8888" assumed_charge="2" index="88"> + <search_result> + <search_hit hit_rank="1" peptide="MNDKNITETERDFNK" peptide_prev_aa="Q" peptide_next_aa="S" protein="tr|O16132|O16132_HYDVU" protein_descr="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="8" tot_num_ions="28" calc_neutral_pep_mass="1835.8467" massdiff="-95.958" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="21.8"/> + <search_score name="nextscore" value="19.1"/> + <search_score name="bscore" value="10.3"/> + <search_score name="yscore" value="8.3"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.48"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00089.00089.2" start_scan="89" end_scan="89" precursor_neutral_mass="1162.6627" assumed_charge="2" index="89"> + <search_result> + <search_hit hit_rank="1" peptide="NSGMSFDFPPK" peptide_prev_aa="K" peptide_next_aa="F" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="10" tot_num_ions="20" calc_neutral_pep_mass="1207.5327" massdiff="-44.870" num_tol_term="2" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="24.4"/> + <search_score name="nextscore" value="17.7"/> + <search_score name="bscore" value="6.5"/> + <search_score name="yscore" value="6.7"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.085"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00090.00090.2" start_scan="90" end_scan="90" precursor_neutral_mass="1398.7382" assumed_charge="2" index="90"> + <search_result> + <search_hit hit_rank="1" peptide="SEPGKQPGEATSSSG" peptide_prev_aa="R" peptide_next_aa="D" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="28" calc_neutral_pep_mass="1399.6217" massdiff="-0.883" num_tol_term="1" num_missed_cleavages="1" is_rejected="0"> + <search_score name="hyperscore" value="21.3"/> + <search_score name="nextscore" value="18.2"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="9.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.38"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00091.00091.2" start_scan="91" end_scan="91" precursor_neutral_mass="1050.5504" assumed_charge="2" index="91"> + <search_result> + <search_hit hit_rank="1" peptide="DYNGLSTSQT" peptide_prev_aa="K" peptide_next_aa="S" protein="sp|P28468|HOX1_HALRO" protein_descr="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="5" tot_num_ions="18" calc_neutral_pep_mass="1066.4567" massdiff="-15.906" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="19.6"/> + <search_score name="nextscore" value="19.4"/> + <search_score name="bscore" value="0"/> + <search_score name="yscore" value="11.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.5"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00092.00092.1" start_scan="92" end_scan="92" precursor_neutral_mass="495.2877" assumed_charge="1" index="92"> + <search_result> + <search_hit hit_rank="1" peptide="SRPGSP" peptide_prev_aa="K" peptide_next_aa="A" protein="sp|P52955|LBX1_MOUSE" protein_descr="Transcription factor LBX1 OS=Mus musculus GN=Lbx1 PE=1 SV=2" num_tot_proteins="1" num_matched_ions="6" tot_num_ions="10" calc_neutral_pep_mass="581.2917" massdiff="-86.004" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="17.8"/> + <search_score name="nextscore" value="16.6"/> + <search_score name="bscore" value="10.9"/> + <search_score name="yscore" value="6.9"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="2.4"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00093.00093.2" start_scan="93" end_scan="93" precursor_neutral_mass="1566.7976" assumed_charge="2" index="93"> + <search_result> + <search_hit hit_rank="1" peptide="TSRCGPHSPLRLGASG" peptide_prev_aa="R" peptide_next_aa="C" protein="tr|Q90853|Q90853_CHICK" protein_descr="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1" num_tot_proteins="1" num_matched_ions="9" tot_num_ions="30" calc_neutral_pep_mass="1576.7897" massdiff="-9.992" num_tol_term="1" num_missed_cleavages="2" is_rejected="0"> + <search_score name="hyperscore" value="22.5"/> + <search_score name="nextscore" value="18.6"/> + <search_score name="bscore" value="7.6"/> + <search_score name="yscore" value="7.4"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="0.071"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00094.00094.1" start_scan="94" end_scan="94" precursor_neutral_mass="501.3357" assumed_charge="1" index="94"> + <search_result> + <search_hit hit_rank="1" peptide="LNPGSV" peptide_prev_aa="K" peptide_next_aa="G" protein="sp|Q04787|BSH_DROME" protein_descr="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="10" calc_neutral_pep_mass="567.3017" massdiff="-65.966" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <search_score name="hyperscore" value="16.3"/> + <search_score name="nextscore" value="14.0"/> + <search_score name="bscore" value="8.6"/> + <search_score name="yscore" value="13.1"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="1.9"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00096.00096.1" start_scan="96" end_scan="96" precursor_neutral_mass="996.6218" assumed_charge="1" index="95"> + <search_result> + <search_hit hit_rank="1" peptide="VLMFCELP" peptide_prev_aa="R" peptide_next_aa="P" protein="tr|O70238|O70238_MOUSE" protein_descr="Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="14" calc_neutral_pep_mass="948.4447" massdiff="48.177" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="3" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="13.2"/> + <search_score name="nextscore" value="11.0"/> + <search_score name="bscore" value="8.7"/> + <search_score name="yscore" value="10.2"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="3.9"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00099.00099.1" start_scan="99" end_scan="99" precursor_neutral_mass="997.0408" assumed_charge="1" index="96"> + <search_result> + <search_hit hit_rank="1" peptide="VLMFCELP" peptide_prev_aa="R" peptide_next_aa="P" protein="tr|O70238|O70238_MOUSE" protein_descr="Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="14" calc_neutral_pep_mass="948.4447" massdiff="48.596" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="3" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="13.0"/> + <search_score name="nextscore" value="11.6"/> + <search_score name="bscore" value="8.6"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="4.7"/> + </search_hit> + </search_result> + </spectrum_query> + <spectrum_query spectrum="mr176-BSA100fmole_BA3_01_8168.d.mgf.00100.00100.1" start_scan="100" end_scan="100" precursor_neutral_mass="996.6215" assumed_charge="1" index="97"> + <search_result> + <search_hit hit_rank="1" peptide="VLMFCELP" peptide_prev_aa="R" peptide_next_aa="P" protein="tr|O70238|O70238_MOUSE" protein_descr="Homeobox protein PSX OS=Mus musculus GN=Rhox6 PE=2 SV=2" num_tot_proteins="1" num_matched_ions="4" tot_num_ions="14" calc_neutral_pep_mass="948.4447" massdiff="48.177" num_tol_term="1" num_missed_cleavages="0" is_rejected="0"> + <modification_info> + <mod_aminoacid_mass position="3" mass="147.0354" /> + </modification_info> + <search_score name="hyperscore" value="13.1"/> + <search_score name="nextscore" value="11.1"/> + <search_score name="bscore" value="8.6"/> + <search_score name="yscore" value="10"/> + <search_score name="cscore" value="0"/> + <search_score name="zscore" value="0"/> + <search_score name="ascore" value="0"/> + <search_score name="xscore" value="0"/> + <search_score name="expect" value="4"/> + </search_hit> + </search_result> + </spectrum_query> + </msms_run_summary> +</msms_pipeline_analysis>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,262 @@ +<?xml version="1.0" encoding="UTF-8"?> +<protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v6.xsd" summary_xml="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml"> +<protein_summary_header reference_database="/Users/icooke/Sources/protk/spec/data/AASequences.fasta" residue_substitution_list="I -> L" source_files="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph.pep.xml" source_files_alt="/Users/icooke/Desktop/iptest/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph.pep.xml" min_peptide_probability="0.20" min_peptide_weight="0.50" num_predicted_correct_prots="14.1" num_input_1_spectra="0" num_input_2_spectra="34" num_input_3_spectra="0" num_input_4_spectra="0" num_input_5_spectra="0" initial_min_peptide_prob="0.05" total_no_spectrum_ids="21.1" sample_enzyme="trypsin"> +<program_details analysis="proteinprophet" time="2014-06-24T07:06:03" version=" Insilicos_LabKey_C++ (TPP v4.7 POLAR VORTEX rev 0, Build 201405141111 (linux))"> +<proteinprophet_details occam_flag="Y" groups_flag="Y" degen_flag="Y" nsp_flag="Y" fpkm_flag="N" initial_peptide_wt_iters="1" nsp_distribution_iters="2" final_peptide_wt_iters="0" run_options="NOPLOT"> + <nsp_information neighboring_bin_smoothing="Y"> + <nsp_distribution bin_no="0" nsp_lower_bound_incl="0.00" nsp_upper_bound_excl="0.10" pos_freq="0.293" neg_freq="0.305" pos_to_neg_ratio="0.96"/> + <nsp_distribution bin_no="1" nsp_lower_bound_incl="0.10" nsp_upper_bound_excl="0.25" pos_freq="0.108" neg_freq="0.108" pos_to_neg_ratio="0.99" alt_pos_to_neg_ratio="0.81"/> + <nsp_distribution bin_no="2" nsp_lower_bound_incl="0.25" nsp_upper_bound_excl="0.50" pos_freq="0.081" neg_freq="0.070" pos_to_neg_ratio="1.16" alt_pos_to_neg_ratio="0.81"/> + <nsp_distribution bin_no="3" nsp_lower_bound_incl="0.50" nsp_upper_bound_excl="1.00" pos_freq="0.138" neg_freq="0.118" pos_to_neg_ratio="1.17"/> + <nsp_distribution bin_no="4" nsp_lower_bound_incl="1.00" nsp_upper_bound_excl="2.00" pos_freq="0.184" neg_freq="0.176" pos_to_neg_ratio="1.05" alt_pos_to_neg_ratio="1.17"/> + <nsp_distribution bin_no="5" nsp_lower_bound_incl="2.00" nsp_upper_bound_excl="5.00" pos_freq="0.086" neg_freq="0.107" pos_to_neg_ratio="0.81" alt_pos_to_neg_ratio="1.17"/> + <nsp_distribution bin_no="6" nsp_lower_bound_incl="5.00" nsp_upper_bound_excl="15.00" pos_freq="0.055" neg_freq="0.061" pos_to_neg_ratio="0.90" alt_pos_to_neg_ratio="1.17"/> + <nsp_distribution bin_no="7" nsp_lower_bound_incl="15.00" nsp_upper_bound_excl="inf" pos_freq="0.054" neg_freq="0.054" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.17"/> + </nsp_information> + <fpkm_information neighboring_bin_smoothing="Y"> + <fpkm_distribution bin_no="0" fpkm_lower_bound_excl="0.00" fpkm_upper_bound_incl="2.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="1" fpkm_lower_bound_excl="2.00" fpkm_upper_bound_incl="4.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="2" fpkm_lower_bound_excl="4.00" fpkm_upper_bound_incl="6.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="3" fpkm_lower_bound_excl="6.00" fpkm_upper_bound_incl="8.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="4" fpkm_lower_bound_excl="8.00" fpkm_upper_bound_incl="10.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="5" fpkm_lower_bound_excl="10.00" fpkm_upper_bound_incl="12.50" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="6" fpkm_lower_bound_excl="12.50" fpkm_upper_bound_incl="15.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="7" fpkm_lower_bound_excl="15.00" fpkm_upper_bound_incl="17.50" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="8" fpkm_lower_bound_excl="17.50" fpkm_upper_bound_incl="20.00" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + <fpkm_distribution bin_no="9" fpkm_lower_bound_excl="20.00" fpkm_upper_bound_excl="inf" pos_freq="0.100" neg_freq="0.100" pos_to_neg_ratio="1.00" alt_pos_to_neg_ratio="1.00"/> + </fpkm_information> + <ni_information> + </ni_information> + <protein_summary_data_filter min_probability="0.00" sensitivity="1.000" false_positive_error_rate="0.327" predicted_num_correct="14" predicted_num_incorrect="7" /> + <protein_summary_data_filter min_probability="0.10" sensitivity="1.000" false_positive_error_rate="0.169" predicted_num_correct="14" predicted_num_incorrect="3" /> + <protein_summary_data_filter min_probability="0.20" sensitivity="1.000" false_positive_error_rate="0.169" predicted_num_correct="14" predicted_num_incorrect="3" /> + <protein_summary_data_filter min_probability="0.30" sensitivity="0.983" false_positive_error_rate="0.132" predicted_num_correct="14" predicted_num_incorrect="2" /> + <protein_summary_data_filter min_probability="0.40" sensitivity="0.983" false_positive_error_rate="0.132" predicted_num_correct="14" predicted_num_incorrect="2" /> + <protein_summary_data_filter min_probability="0.50" sensitivity="0.949" false_positive_error_rate="0.107" predicted_num_correct="13" predicted_num_incorrect="2" /> + <protein_summary_data_filter min_probability="0.60" sensitivity="0.949" false_positive_error_rate="0.107" predicted_num_correct="13" predicted_num_incorrect="2" /> + <protein_summary_data_filter min_probability="0.70" sensitivity="0.901" false_positive_error_rate="0.090" predicted_num_correct="13" predicted_num_incorrect="1" /> + <protein_summary_data_filter min_probability="0.80" sensitivity="0.795" false_positive_error_rate="0.064" predicted_num_correct="11" predicted_num_incorrect="1" /> + <protein_summary_data_filter min_probability="0.90" sensitivity="0.622" false_positive_error_rate="0.024" predicted_num_correct="9" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="0.95" sensitivity="0.556" false_positive_error_rate="0.018" predicted_num_correct="8" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="0.96" sensitivity="0.421" false_positive_error_rate="0.009" predicted_num_correct="6" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="0.97" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="0.98" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="0.99" sensitivity="0.352" false_positive_error_rate="0.004" predicted_num_correct="5" predicted_num_incorrect="0" /> + <protein_summary_data_filter min_probability="1.00" sensitivity="0.000" false_positive_error_rate="0.000" predicted_num_correct="0" predicted_num_incorrect="0" /> +</proteinprophet_details> +</program_details> +</protein_summary_header> +<dataset_derivation generation_no="0"> +</dataset_derivation> +<protein_group group_number="1" probability="0.9996"> + <protein protein_name="sp|P22807|SLOU_DROME" n_indistinguishable_proteins="1" probability="0.9996" percent_coverage="8.3" unique_stripped_peptides="FIISANGAAVAGKQE+FKTTRYLSVCER+LVAAVAARTTQASST+SDIDDPSSETDSK" group_sibling_id="a" total_number_peptides="5" pct_spectrum_ids="17.10" confidence="0.87"> + <parameter name="prot_length" value="659"/> + <annotation protein_description="Homeobox protein slou OS=Drosophila melanogaster GN=slou PE=2 SV=1"/> + <peptide peptide_sequence="LVAAVAARTTQASST" charge="2" initial_probability="0.9740" nsp_adjusted_probability="0.9776" fpkm_adjusted_probability="0.9776" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.83" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="1.30" is_contributing_evidence="Y" calc_neutral_pep_mass="1427.7737"> + </peptide> + <peptide peptide_sequence="FIISANGAAVAGKQE" charge="2" initial_probability="0.8584" nsp_adjusted_probability="0.8760" fpkm_adjusted_probability="0.8760" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.95" n_sibling_peptides_bin="4" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.86" is_contributing_evidence="Y" calc_neutral_pep_mass="1456.7677"> + </peptide> + <peptide peptide_sequence="SDIDDPSSETDSK" charge="2" initial_probability="0.8343" nsp_adjusted_probability="0.8543" fpkm_adjusted_probability="0.8543" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.97" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="1.31" is_contributing_evidence="Y" calc_neutral_pep_mass="1376.5577"> + </peptide> + <peptide peptide_sequence="FKTTRYLSVCER" charge="2" initial_probability="0.1399" nsp_adjusted_probability="0.1399" fpkm_adjusted_probability="0.1399" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="2.67" n_sibling_peptides_bin="5" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.14" is_contributing_evidence="N" calc_neutral_pep_mass="1483.7607"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="2" probability="0.9990"> + <protein protein_name="sp|Q04787|BSH_DROME" n_indistinguishable_proteins="1" probability="0.9990" percent_coverage="3.5" unique_stripped_peptides="SEPGKQPGEATSSSG" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="9.45" confidence="0.23"> + <parameter name="prot_length" value="429"/> + <annotation protein_description="Brain-specific homeobox protein OS=Drosophila melanogaster GN=bsh PE=2 SV=5"/> + <peptide peptide_sequence="SEPGKQPGEATSSSG" charge="2" initial_probability="0.9990" nsp_adjusted_probability="0.9990" fpkm_adjusted_probability="0.9990" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="2.00" is_contributing_evidence="Y" calc_neutral_pep_mass="1399.6217"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="3" probability="0.9939"> + <protein protein_name="sp|P28468|HOX1_HALRO" n_indistinguishable_proteins="1" probability="0.9939" percent_coverage="4.7" unique_stripped_peptides="EERTNNITTMAMK+NRAVFSLMQRR+NSGMSFDFPPK" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="10.06" confidence="0.54"> + <parameter name="prot_length" value="741"/> + <annotation protein_description="Homeobox protein AHox1 OS=Halocynthia roretzi GN=AHOX1 PE=2 SV=1"/> + <peptide peptide_sequence="NSGMSFDFPPK" charge="2" initial_probability="0.9488" nsp_adjusted_probability="0.9557" fpkm_adjusted_probability="0.9557" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="1.18" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.95" is_contributing_evidence="Y" calc_neutral_pep_mass="1207.5327"> + </peptide> + <peptide peptide_sequence="EERTNNITTMAMK" charge="2" initial_probability="0.6481" nsp_adjusted_probability="0.6821" fpkm_adjusted_probability="0.6821" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.48" n_sibling_peptides_bin="4" max_fpkm="108106074808565001639284951201340339017093864540219515696523998091203710034133539363830907323547648.00" fpkm_bin="1296125268" n_instances="1" exp_tot_instances="0.65" is_contributing_evidence="Y" calc_neutral_pep_mass="1501.7017"> +<modification_info modified_peptide="E[111]ERTNNITTMAMK"> +<mod_aminoacid_mass position="1" mass="111.032000"/> +</modification_info> + </peptide> + <peptide peptide_sequence="NRAVFSLMQRR" charge="2" initial_probability="0.5301" nsp_adjusted_probability="0.5679" fpkm_adjusted_probability="0.5679" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.60" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.53" is_contributing_evidence="Y" calc_neutral_pep_mass="1374.7307"> +<modification_info modified_peptide="NRAVFSLM[147]QRR"> +<mod_aminoacid_mass position="8" mass="147.035400"/> +</modification_info> + </peptide> + </protein> +</protein_group> +<protein_group group_number="4" probability="0.9938"> + <protein protein_name="sp|O35767|NKX25_RAT" n_indistinguishable_proteins="1" probability="0.9938" percent_coverage="10.7" unique_stripped_peptides="PDPAKDPRADK+QDQTLELLGPPP+SLAAGDLSARL" group_sibling_id="a" total_number_peptides="3" pct_spectrum_ids="8.52" confidence="0.76"> + <parameter name="prot_length" value="318"/> + <annotation protein_description="Homeobox protein Nkx-2.5 OS=Rattus norvegicus GN=Nkx2-5 PE=2 SV=1"/> + <peptide peptide_sequence="PDPAKDPRADK" charge="2" initial_probability="0.9741" nsp_adjusted_probability="0.9777" fpkm_adjusted_probability="0.9777" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.83" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1190.6047"> + </peptide> + <peptide peptide_sequence="SLAAGDLSARL" charge="2" initial_probability="0.6075" nsp_adjusted_probability="0.6433" fpkm_adjusted_probability="0.6433" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.19" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.61" is_contributing_evidence="Y" calc_neutral_pep_mass="1054.5767"> + </peptide> + <peptide peptide_sequence="QDQTLELLGPPP" charge="2" initial_probability="0.2197" nsp_adjusted_probability="0.2197" fpkm_adjusted_probability="0.2197" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="1.58" n_sibling_peptides_bin="4" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.22" is_contributing_evidence="Y" calc_neutral_pep_mass="1271.6397"> +<modification_info modified_peptide="Q[111]DQTLELLGPPP"> +<mod_aminoacid_mass position="1" mass="111.032100"/> +</modification_info> + </peptide> + </protein> +</protein_group> +<protein_group group_number="5" probability="0.9918"> + <protein protein_name="tr|O35455|O35455_MOUSE" n_indistinguishable_proteins="1" probability="0.9918" percent_coverage="13.1" unique_stripped_peptides="ALPTTLAMRAAAPAPAPAP+QPLPGSDVAAFLVPT" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="7.38" confidence="0.70"> + <parameter name="prot_length" value="260"/> + <annotation protein_description="Homeobox protein Nkx2.6 (Fragment) OS=Mus musculus GN=Nkx2-6 PE=2 SV=1"/> + <peptide peptide_sequence="ALPTTLAMRAAAPAPAPAP" charge="2" initial_probability="0.9747" nsp_adjusted_probability="0.9782" fpkm_adjusted_probability="0.9782" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.59" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1768.9657"> + </peptide> + <peptide peptide_sequence="QPLPGSDVAAFLVPT" charge="2" initial_probability="0.5852" nsp_adjusted_probability="0.6217" fpkm_adjusted_probability="0.6217" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.97" n_sibling_peptides_bin="3" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.59" is_contributing_evidence="Y" calc_neutral_pep_mass="1492.7927"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="6" probability="0.9671"> + <protein protein_name="tr|Q90853|Q90853_CHICK" n_indistinguishable_proteins="1" probability="0.9671" percent_coverage="4.3" unique_stripped_peptides="TSRCGPHSPLRLGASG" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.58" confidence="0.25"> + <parameter name="prot_length" value="368"/> + <annotation protein_description="Homeobox protein OS=Gallus gallus GN=GH6 PE=2 SV=1"/> + <peptide peptide_sequence="TSRCGPHSPLRLGASG" charge="2" initial_probability="0.9683" nsp_adjusted_probability="0.9671" fpkm_adjusted_probability="0.9671" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.97" is_contributing_evidence="Y" calc_neutral_pep_mass="1576.7897"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="7" probability="0.9582"> + <protein protein_name="sp|P22711|TIN_DROME" n_indistinguishable_proteins="1" probability="0.9582" percent_coverage="2.4" unique_stripped_peptides="KLNLSATQVK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.54" confidence="0.22"> + <parameter name="prot_length" value="416"/> + <annotation protein_description="Muscle-specific homeobox protein tinman OS=Drosophila melanogaster GN=tin PE=2 SV=2"/> + <peptide peptide_sequence="KLNLSATQVK" charge="2" initial_probability="0.9597" nsp_adjusted_probability="0.9582" fpkm_adjusted_probability="0.9582" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.96" is_contributing_evidence="Y" calc_neutral_pep_mass="1082.6447"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="8" probability="0.9558"> + <protein protein_name="sp|Q26604|SMOX5_SCHMA" n_indistinguishable_proteins="1" probability="0.9558" percent_coverage="5.3" unique_stripped_peptides="TQPPSISNILPSSLK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.53" confidence="0.31"> + <parameter name="prot_length" value="284"/> + <annotation protein_description="Homeobox protein SMOX-5 OS=Schistosoma mansoni GN=SMOX-5 PE=2 SV=1"/> + <peptide peptide_sequence="TQPPSISNILPSSLK" charge="2" initial_probability="0.9574" nsp_adjusted_probability="0.9558" fpkm_adjusted_probability="0.9558" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.96" is_contributing_evidence="Y" calc_neutral_pep_mass="1562.8667"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="9" probability="0.9265"> + <protein protein_name="sp|Q01702|DLX3B_DANRE" n_indistinguishable_proteins="1" probability="0.9265" percent_coverage="3.3" unique_stripped_peptides="EEPETEVRM" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="4.39" confidence="0.31"> + <parameter name="prot_length" value="269"/> + <annotation protein_description="Homeobox protein Dlx3b OS=Danio rerio GN=dlx3b PE=2 SV=1"/> + <peptide peptide_sequence="EEPETEVRM" charge="2" initial_probability="0.9292" nsp_adjusted_probability="0.9265" fpkm_adjusted_probability="0.9265" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.93" is_contributing_evidence="Y" calc_neutral_pep_mass="1100.4807"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="10" probability="0.8221"> + <protein protein_name="sp|P34663|HM23_CAEEL" n_indistinguishable_proteins="1" probability="0.8221" percent_coverage="3.9" unique_stripped_peptides="SPNLPFSATIPR" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.91" confidence="0.23"> + <parameter name="prot_length" value="305"/> + <annotation protein_description="Homeobox protein ceh-23 OS=Caenorhabditis elegans GN=ceh-23 PE=2 SV=1"/> + <peptide peptide_sequence="SPNLPFSATIPR" charge="2" initial_probability="0.8278" nsp_adjusted_probability="0.8221" fpkm_adjusted_probability="0.8221" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.83" is_contributing_evidence="Y" calc_neutral_pep_mass="1280.6877"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="11" probability="0.8155"> + <protein protein_name="tr|Q23819|Q23819_HYDVD" n_indistinguishable_proteins="1" probability="0.8155" percent_coverage="12.1" unique_stripped_peptides="LQLKQNNAKGSGIK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.88" confidence="0.45"> + <parameter name="prot_length" value="116"/> + <annotation protein_description="Cnox3 protein (Fragment) OS=Hydra viridissima GN=cnox3 PE=2 SV=1"/> + <peptide peptide_sequence="LQLKQNNAKGSGIK" charge="2" initial_probability="0.8214" nsp_adjusted_probability="0.8155" fpkm_adjusted_probability="0.8155" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.82" is_contributing_evidence="Y" calc_neutral_pep_mass="1479.8517"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="12" probability="0.8110"> + <protein protein_name="tr|Q9YHC2|Q9YHC2_CHICK" n_indistinguishable_proteins="1" probability="0.8110" percent_coverage="14.4" unique_stripped_peptides="IAQLLKKHKPGAG+KHKPGAGGLLPHPAEG" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="4.97" confidence="0.55"> + <parameter name="prot_length" value="153"/> + <annotation protein_description="Homeodomain protein (Fragment) OS=Gallus gallus GN=Nkx-6.1 PE=2 SV=1"/> + <peptide peptide_sequence="KHKPGAGGLLPHPAEG" charge="2" initial_probability="0.7800" nsp_adjusted_probability="0.7409" fpkm_adjusted_probability="0.7409" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.27" n_sibling_peptides_bin="2" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.78" is_contributing_evidence="Y" calc_neutral_pep_mass="1546.8367"> + </peptide> + <peptide peptide_sequence="IAQLLKKHKPGAG" charge="2" initial_probability="0.2705" nsp_adjusted_probability="0.2705" fpkm_adjusted_probability="0.2705" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.78" n_sibling_peptides_bin="3" max_fpkm="179430918457452872074560764997795840.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.27" is_contributing_evidence="Y" calc_neutral_pep_mass="1341.8247"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="13" probability="0.7912"> + <protein protein_name="tr|Q24785|Q24785_9METZ" n_indistinguishable_proteins="1" probability="0.7912" percent_coverage="5.7" unique_stripped_peptides="TQLIALERK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.77" confidence="0.36"> + <parameter name="prot_length" value="157"/> + <annotation protein_description="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox3 PE=3 SV=1"/> + <peptide peptide_sequence="TQLIALERK" charge="2" initial_probability="0.7977" nsp_adjusted_probability="0.7912" fpkm_adjusted_probability="0.7912" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.80" is_contributing_evidence="Y" calc_neutral_pep_mass="1052.6347"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="14" probability="0.7078"> + <protein protein_name="tr|Q24786|Q24786_9METZ" n_indistinguishable_proteins="1" probability="0.7078" percent_coverage="11.0" unique_stripped_peptides="AVQKYLTAHEQSK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.38" confidence="0.37"> + <parameter name="prot_length" value="118"/> + <annotation protein_description="Homeobox-containing protein (Fragment) OS=Ephydatia fluviatilis GN=prox1 PE=3 SV=1"/> + <peptide peptide_sequence="AVQKYLTAHEQSK" charge="2" initial_probability="0.7159" nsp_adjusted_probability="0.7078" fpkm_adjusted_probability="0.7078" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.72" is_contributing_evidence="Y" calc_neutral_pep_mass="1483.7787"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="15" probability="0.6690"> + <protein protein_name="tr|O16132|O16132_HYDVU" n_indistinguishable_proteins="1" probability="0.6690" percent_coverage="4.6" unique_stripped_peptides="MNDKNITETERDFNK" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="3.20" confidence="0.17"> + <parameter name="prot_length" value="328"/> + <annotation protein_description="NK-2 class homeobox transcription factor OS=Hydra vulgaris GN=CnNK-2 PE=2 SV=1"/> + <peptide peptide_sequence="MNDKNITETERDFNK" charge="2" initial_probability="0.6777" nsp_adjusted_probability="0.6690" fpkm_adjusted_probability="0.6690" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="-2.00" fpkm_bin="1588330504" n_instances="1" exp_tot_instances="0.68" is_contributing_evidence="Y" calc_neutral_pep_mass="1835.8467"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="16" probability="0.4795"> + <protein protein_name="sp|O88181|BARH2_RAT" n_indistinguishable_proteins="2" probability="0.4795" percent_coverage="2.3" unique_stripped_peptides="RQTAVGLEL" group_sibling_id="a" total_number_peptides="1" pct_spectrum_ids="2.31" confidence="0.11"> + <parameter name="prot_length" value="384"/> + <annotation protein_description="BarH-like 2 homeobox protein OS=Rattus norvegicus GN=Barhl2 PE=2 SV=1"/> + <indistinguishable_protein protein_name="sp|Q24255|BARH1_DROME"> + <annotation protein_description="Homeobox protein B-H1 OS=Drosophila melanogaster GN=B-H1 PE=2 SV=2"/> + </indistinguishable_protein> + <peptide peptide_sequence="RQTAVGLEL" charge="2" initial_probability="0.4894" nsp_adjusted_probability="0.4795" fpkm_adjusted_probability="0.4795" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.49" is_contributing_evidence="Y" calc_neutral_pep_mass="967.5447"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="17" probability="0.2438"> + <protein protein_name="tr|Q90263|Q90263_DANRE" n_indistinguishable_proteins="1" probability="0.2438" percent_coverage="5.2" unique_stripped_peptides="PENLLLHGPFSR" group_sibling_id="a" total_number_peptides="2" pct_spectrum_ids="1.87" confidence="0.10"> + <parameter name="prot_length" value="233"/> + <annotation protein_description="Empty spiracles homeobox 3 OS=Danio rerio GN=emx3 PE=2 SV=1"/> + <peptide peptide_sequence="PENLLLHGPFSR" charge="2" initial_probability="0.2511" nsp_adjusted_probability="0.2438" fpkm_adjusted_probability="0.2438" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="2" exp_tot_instances="0.40" is_contributing_evidence="Y" calc_neutral_pep_mass="1360.7247"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="18" probability="0.0000"> + <protein protein_name="sp|Q22909|HM30_CAEEL" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="RQATSGMDLLS" group_sibling_id="a" total_number_peptides="0" confidence="0.0803"> + <parameter name="prot_length" value="237"/> + <annotation protein_description="Homeobox protein ceh-30 OS=Caenorhabditis elegans GN=ceh-30 PE=2 SV=2"/> + <peptide peptide_sequence="RQATSGMDLLS" charge="2" initial_probability="0.1644" nsp_adjusted_probability="0.1591" fpkm_adjusted_probability="0.1591" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.16" is_contributing_evidence="N" calc_neutral_pep_mass="1175.5607"> +<modification_info modified_peptide="RQATSGM[147]DLLS"> +<mod_aminoacid_mass position="7" mass="147.035400"/> +</modification_info> + </peptide> + </protein> +</protein_group> +<protein_group group_number="19" probability="0.0000"> + <protein protein_name="tr|O77024|O77024_EPHMU" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="ETEMEMK" group_sibling_id="a" total_number_peptides="0" confidence="0.0790"> + <parameter name="prot_length" value="166"/> + <annotation protein_description="EmH-3 (Fragment) OS=Ephydatia muelleri GN=EmH-3 PE=3 SV=1"/> + <peptide peptide_sequence="ETEMEMK" charge="2" initial_probability="0.0906" nsp_adjusted_probability="0.0874" fpkm_adjusted_probability="0.0874" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.09" is_contributing_evidence="N" calc_neutral_pep_mass="892.3307"> +<modification_info modified_peptide="E[111]TEM[147]EM[147]K"> +<mod_aminoacid_mass position="1" mass="111.032000"/> +<mod_aminoacid_mass position="4" mass="147.035400"/> +<mod_aminoacid_mass position="6" mass="147.035400"/> +</modification_info> + </peptide> + </protein> +</protein_group> +<protein_group group_number="20" probability="0.0000"> + <protein protein_name="tr|Q23824|Q23824_HYDVD" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="SKEAEIEESVR" group_sibling_id="a" total_number_peptides="0" confidence="0.0908"> + <parameter name="prot_length" value="128"/> + <annotation protein_description="Msh protein (Fragment) OS=Hydra viridissima GN=msh PE=2 SV=1"/> + <peptide peptide_sequence="SKEAEIEESVR" charge="2" initial_probability="0.1145" nsp_adjusted_probability="0.1105" fpkm_adjusted_probability="0.1105" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="2" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.11" is_contributing_evidence="N" calc_neutral_pep_mass="1257.6197"> + </peptide> + </protein> +</protein_group> +<protein_group group_number="21" probability="0.0000"> + <protein protein_name="tr|Q9YH59|Q9YH59_CHICK" n_indistinguishable_proteins="1" probability="0.0000" unique_stripped_peptides="FMAPSSGMNMGGMGG" group_sibling_id="a" total_number_peptides="0" confidence="0.0611"> + <parameter name="prot_length" value="344"/> + <annotation protein_description="Homeodomain protein NKx2.1 OS=Gallus gallus GN=NKx2.1 PE=2 SV=1"/> + <peptide peptide_sequence="FMAPSSGMNMGGMGG" charge="2" initial_probability="0.0864" nsp_adjusted_probability="0.0833" fpkm_adjusted_probability="0.0833" weight="1.00" group_weight="1.00" is_nondegenerate_evidence="Y" n_enzymatic_termini="1" n_sibling_peptides="0.00" n_sibling_peptides_bin="0" max_fpkm="0.00" fpkm_bin="0" n_instances="1" exp_tot_instances="0.09" is_contributing_evidence="N" calc_neutral_pep_mass="1460.5197"> +<modification_info modified_peptide="FM[147]APSSGMNM[147]GGM[147]GG"> +<mod_aminoacid_mass position="2" mass="147.035400"/> +<mod_aminoacid_mass position="10" mass="147.035400"/> +<mod_aminoacid_mass position="13" mass="147.035400"/> +</modification_info> + </peptide> + </protein> +</protein_group> +</protein_summary>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="protk" version="1.4.3"> + <repository changeset_revision="2b240f1be1ce" name="package_protk_1_4_3" owner="iracooke" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="trans_proteomic_pipeline" version="4.8.0"> + <repository changeset_revision="3d56da50b195" name="package_tpp_4_8_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>